The Adventure Time: Banana Guard Academy miniseries confirms hints elsewhere in the franchise that the Bananas are a bunch of racist fruit who consider themselves to be the only people fit for police work, and refuse to allow their women to date other kinds of Candy Person.
Enzo: Get over it, Redbeard. As long as we look different, things aren't going to change.
As a child, Aquaman was exiled from his home due to people with blonde hair being discriminated against in Atlantis.
DC Atlanteans in general have proven themselves to be superstitious, racist jerks, sometimes with humanoid Atlanteans even targeting non human, more fish-like Atlanteans for being impure.
Aqualad's origin involves being discriminated against for his purple eyes.
Frequently, Atlanteans are borderline genocidal against people living on the surface. It's telling that in New 52 continuity, Ocean Master's distaste for humans still makes him more tolerant than some of his followers. Though Ocean Master would grow to reconsider his prejudices after escaping a surface-world prison and taking residence with a human woman and her son.
The Young Justice tie-in comic explains that human-looking Atlanteans are prized and thought of as pure (since they descended from the humans who lived on Atlantis before it sank), while the more fish-like creatures such as Lagoon Boy and King Shark are subject to various forms of racial discrimination. Aqualad is subject to this as well, since he was surgically given artificial gills and webbed fingers and toes to survive underwater.
In BB Wolf and the 3 LPs, a retelling of the Three Little Pigs set in the 1920s South, wolves are socially, legally, and economically discriminated against by a ruling class of wealthy pigs. The pigs demand the wolf protagonist's farm and murder his family when he refuses to sell, sending him on a Roaring Rampage of Revenge.
Bamse: The two most notable are the ones about Kalle Svartskalle, a hedgehog with black spines on his head, and "Något luktar—men vad?", where two of the villains try to drive out a family of skunks as expies of The Klan.
A Talking Animal versions of this trope occurs in Blacksad: species isn't a problem in this world, but color is, as in literal fur color. The main two groups are Arctic Nation, a semi-religious association of white-coated animals with a stylized snowflake as a symbol, and the Claws, a street gang of black-furred beasts. John Blacksad himself, the protagonist, is a black-and-white cat, so neither side likes him. Not much discussion is given to what they think of animals with fur colors other than black or white, though - the two groups mostly seem to focus on hating each other. In another Blacksad story there was similar tension between lizards and mammals ( a mangoose ended up in a reptilian bar chasing a lizard that double crossed his boss, all the patrons close in on him).
Brave Chef Brianna: Humans vs. Monsters. Madame Cron was so affected by what she suffered from humans she antagonizes Brianna out of a desire to protect herself and her fellow monsters from humans.
Copperhead takes place shortly after a war between humans and Boo's species. Boo claims that this is why he didn't get the permanent sheriff position: human bureaucrats didn't want an alien holding authority over a (mostly) human community.
Inverted in the first issue of Demon Knights, where Al Jabr (an Arab swordsman) is denied service at a European pub due to his race. Exoristos (a white Amazon) sees this and asks if she is allowed service, and then angrily points out the bartender's hypocrisy when he tells her yes. She claims that despite the color of his skin, Jabr has far more in common with the white bar patrons than she does, seeing as how she comes from a mystical society of immortal warrior women.
Exaggerated in Dinocorps with the Saurons. The Saurons are a group of dinosaurs who consider themselves to be "True-Bloods," and they hated how the other dinosaurs used so much technology to make their community thrive. Jarek, the leader of the Saurons, sent an entire species into extinction simply because they weren't Saurons like him. When he wakes up in the present and discovers humans (or mammals as he calls them) have taken over, he immediately decides to kill them all too so he can rule the planet with fellow Saurons.
In Five Weapons, psionics are ignored by the assassin community as superstitious nonsense and is refused the right to have their own weapons club.
Averted in one issue of IDW's Ghostbusters (2013) after Egon tried using a gris-gris bag from New Orleans to save Janine's soul from Viking ghosts and one of said ghosts accused Egon of using magic against them.
Egon: I didn't use magic, I was merely concerned that an evil spirit may have bewitchedthe woman and brought forth a protective talisman as a precaution.
Viking Ghost: Do we look like evil spirits to you, Sorcerer?
Henry Pym indulges in a bit when he talks about Skrulls, which he calls an untrustworthy, treacherous and ruthless species while the Kree are a noble race even if they do tend to look at humans like they were cavemen. Somewhat justified for Pym in that he had just been rescued from captivity by the Skrulls and over the years he's worked with a number of Kree heroes including Captain Mar-vell.
In the Hellboy comics, some occasional anti-demon sentiment is present (well, that's to be expected). In one of the issues of the B.P.R.D. spin-off, an agent is called out for being a "speciest" after making derogatory remarks about Abe Sapien.
For the longest time in Judge Dredd, mutants were forced to struggle to survive in the cursed earth because they were banned from entering the Mega-Cities. When Dredd himself managed to overturn this law, he suffers a reduction in rank and civil unrest plagues Mega-City One. Then, 2009's "Tour of Duty" storyline involved an effort to relocate mutants to outside ghettos where they would produce food for normals, with Dredd himself being unofficially exiled as punishment for letting them in in the first place.
Done pretty blatantly in the EC Comics story "Judgement Day", with its orange and blue robots. They are identical but for outer casings and programming, but the blue robots sit at the back of the bus, recharge in different stations, live in their own sector in town. The human evaluating the robot society does not let them progress to space until they can get over that, noting that Earth was like this once, and only owned the universe after humans learned to live together. In the last panel of the story he takes off his helmet, revealing that he is black.
Kind of crosses over with Some Anvils Need to Be Dropped and a real life example when the Comics Code Authority tried to tell EC editor Bill Gaines that the hero could not be black.
Kling Klang Klatch takes it to a whole new level: a town of talking teddy bears stews race hate, with a minority of stuffed panda bears locked in mutual disdain with the regular teddies. There are other toys in this world: everyone's got someone to look down on, if only the drugged-out raggedy-anne dolls.
In the Marvel Universe the Kree are an extraterrestrial race that have conquered many worlds. The Kree are divided into a majority population that is indistinguishable from humans of European descent and a population with blue skin. The blue skinned Kree view themselves as superior to the 'pink' skinned Kree and dominate the high ranking positions in the military and government. The thing with the Kree is that the blue-skin Kree are what the Kree originally look like, the caucasian looking Kree came about later only through genetic engineering in order to break through the Kree's evolutionary dead-end (which was a failure), and so they see the blue Kree as 'pure-blooded'.
During The Kree/Skrull War, the government proposed rounding up aliens living on Earth and forcing them into camps. After Nick Fury allowed Captain Mar-Vell to escape capture, he attempted to justify his actions by saying that he remembered the Japanese American internment camps from World War II, and vowed never to let something like that occur on U.S. soil ever again.
Similarly, Marvel Atlanteans have blue skin, but half-Atlanteans like Namor have the skin tone of their human parents (which in this case is Caucasian). In The Blue Marvel, it's established that when Namor was growing up in Atlantis, the other kids called him "pale crab" and ostracized him for his color. His experiences are specifically compared to those of the Blue Marvel, a black hero who faced discrimination in his 1960s heyday.
Most aliens in the Marvel universe regard humans as psychotic and primitive cave men, while having a healthy respect/fear for what they're capable of.
Humans seem to be increasingly developing this sort of attitude toward aliens too now- including some superheroes- particularly after extraterrestrials repeated attempts to invade Earth.
Gladiator is sometimes this trope, though it seemed to have worn off - he sent his son to the Jean Grey School. It may have recurred recently in him because of him being a Proud Warrior Race Guy and the epic beating he suffered at the hands of the Phoenix Five.
The Reboot also had the White Triangle, a group of speciesists composed of several species who are all ultimately pawns of a Nazi-esque regime-slash-religion that claims Daxamites are superior to all other species. Since Daxamites basically have all the powers of Kryptonians, they have some reason for assuming so - but in addition to being racist, they're also dirt-ignorant, superstitious, inbred, violent Jerk Ass thugs. Who can melt entire planets into slag, from orbit, by looking at them funny.
The "revised original" version of Legion had a pretty important storyline: "Superman and the Legion of Superheroes". Not only did humans start putting aliens in concentration camps and kill them, but after Earth withdrew from the United Planets, nearly all of the different species decried Earth as "ignorant and backwater" and some even tried to lock up and kill anyone associated with Earth. The story ended with Supes and the Legion calling out both sides.
The original LSH had a story about how 'Shadow Lass' arrives from Talok to explain that her world has been conquered quietly by the Fatal Five. To infiltrate unnoticed, the Legionnaires adopt the identities of a rag-wearing desert-living minority. Later, it is revealed Shady is one of these people; she is slightly darker blue than the city folk. Lampshaded in a later story by having Shady look slightly African, while being blue, and dressed for the desert (think Arab).
In the Limited Series, Secrets of the Legion of Super-Heroes, Chameleon Boy is a Durlanian, a shapeshifting species that were treated with mistrust and prejudice by most other species for their abilities. He wanted to provide a good example to contradict that prejudice and applied for membership into the Legion to accomplish that. For their part, the Legion was all in favor of his goals and inducted him in without a problem.
One of the story arcs in L.E.G.I.O.N. '89 revolved around an alien civil war. Several issues in, a member of L.E.G.I.O.N. admits they can't tell what divides the two sides. Turns out they have different eye colors.
Most animosity between species in Mouse Guard is not this trope, instead being based on the very real problems of predator/prey relationships or acting as competitors or "pests" for other species. Breaking from this, there's the relationship between Bats and the other species. Bats are distrusted by the other species. (according to the Bats' accounts, this dates back to time immemorial, when neither side in a war between birds and land animals would accept their help, the birds considering them land animals because they had fur, and the land animals being suspicious of their wings) For their part, the bats hate the other species in return and will react with extreme violence to any suggestion that they're not trustworthy.
The Termight in Nemesis the Warlock is the Spanish Inquisition IN SPACE! and will kill any and all aliens on sight. Even the main antagonist, Tomas de Torquemada is a descendant of the original Torquemada with a few rounds of Historical Villain Upgrades. It is revealed that both Torquemadas are reincarnations of the same individual. Other reincarnations apparently include Adolf Hitler. At one point Torquemada from the future meets his historical namesake and accidentally ends up in the torture chambers of Spanish Inquisition under the watchful eyes of the original Torquemada. While Torquemada from the future describes his exploits to the original Torquemada in detail, the Inquisition keeps torturing him. Torquemada finds the experience painful and traumatic. The original one, that is.
Torquemada's Inquisitors are faced with a dilemma. Having suceeded only too well in "purifying" Earth and the immediate Galaxy of sentient aliens, with nobody else left to kill, they wonder how to keep the machine working and sustaining the hatred and xenophobic fear which keeps them in power. Then they have the brilliant idea to go back to basics and purify the human race still further by selecting a new hate-group. The new pogrom is against people with red hair and freckles. note This Lampshades the often-overlooked reality that any bureaucracy always finds reasons to perpetuate itself; the Nazi death camps would not have said "well done, job completed" and wound themselves up when there were no Jews left. They'd have moved on to other forms of hated "subhuman" who were next on the list, as was seen with gypsies. The nazis also had plans for Slavs and black people, whi were not seen as being so high a priority after Jews. They were simply timed out by My 1945.
Jack Kirby's New Gods lived in a city that was over the home of a group of bug people who were quite blatantly treated with direct racism by the Gods even after one of their own, Forager, became an ally.
Aaron Stack from Nextwave was awfully 'racist' about how awesome robots are compared to 'fleshy' humans. It didn't stop him from trying to save them, oddly enough. In fairness, Machine Man (Aaron) has spent his entire life being the target of anti-robot prejudice, with people trying to kill him and viewing his life as valueless because he's a machine. By now, he has become very bitter (as well as seriously depressed) about it and can give at least as good as he gets in the insult department.
Owly sometimes has undercurrents of this, with other creatures the eponymous Owly meets assuming the worst of him because he's an owl, and they usually eat smaller animals, rather than trying to befriend them. A Little Blue, in particular, entirely revolves around the interactions between Owly and a bluejay that initially assumes that every action Owly takes, no matter how benevolent or selfless, has a sinister ulterior motive.
The gimmick of Crux from Red Hood and the Outlaws, a human bent on killing every alien on Earth. He has a special hatred for Tamaraneans, blaming them for the death of his parents after they were killed by the crash of a Tamaranean war cruiser, directly into their car, as he sat in the backseat.
He just lucked out as his parents were highly respected alien researchers.
Runaways includes Skrulls VS Majesdanians (Karolina's species) and Skrulls VS machines. The Skrull Empire (or at least, the outpost Xavin comes from) has been at war with Majesdane for generations. Xavin and Karolina attempted to end this using their Arranged Marriage, but it did not take. When a group of Majesdanians who hold Karolina responsible for her parents' role in starting the war come looking for her, they find her relationship with Xavin disgusting. Their inter-species relationship was used as an allegory for homosexuality/interracial relationships and transgender issues throughout the comics run. Xavin, for his/her part, has trouble thinking of machines as equals, which causes some friction with her cyborg teammate Victor. It ranges from being unthinkingly condescending (calling him the 'house android') to being a full-on Jerkass, though she gradually gets better.
Frank in Scarlet Veronica is racist against zombies. He calls them "flesh-chuckin' grave apes". The fact that he himself is a Frankenstein's Monster and thus not too far removed from a zombie turns this into Hypocritical Humor.
The Echidnas, who became the first to be civilized, looked down on everyone. Still did until Eggman wiped most of their population out and Thrash tossed the rest into another Zone.
Overlanders, four-fingered humans, were shown to be incredibly war-like and bloodthirsty. It's obvious both Robotniks did nothing to improve that image.
Machines in particular. Naugus, on two separate instances, gleeflly ramped up the hate of them in Mobians, leading to a brief Civil War between Mobians and Robians (roboticized Mobians) and the AI NICOLE being temporarily exiled.
Not based on race, but the same basic idea is the reason why the Dark Legion broke off from the rest of Echidna society. Their love of technology led to them being persecuted and oppressed by the government.
The members of the Battle Bird Armada are a mild example of this. They feel that since they can fly naturally, only they have the right to be in the sky, and everyone else should stay on the ground. One member, Speedy, seems to particularly hate Tails, due to his ability to fly naturally despite not being a bird.
Speedy: That's right, freak. Crawl. Crawl on the ground where you belong.
We learn through a flashback in "The Trial Of Gefforey St. John" that Ixis Naugus was able to convince Gefforey into becoming his student by playing off of Gefforey's resentment of Overlanders (Gefforey's father was a soldier in the Great War and was killed by Overlanders during a mission). It would seem that Mobian/Overlander hatred may not be entirely gone yet.
New 52 Supergirl hated clones, believing that they inevitably turn evil, which proved unfortunate for Superboy, whose very existence revolted her - though she pitied him more than anything else. This turns out to be a learned prejudice, one held by Kryptonians at large due to the Kryptonian Clone Revolt. The events of H'el on Earth caused her to re-examine this prejudice and unlearn it, and when she runs into Superboy again in issue 38 and he's attacked, she immediately jumps to his defence.
In the Red Daughter of Krypton arc, Red Lantern Zilius Zox, a spherical alien, don't like a lot non-round aliens. He disliked Green Lantern B'ox instantly just because B'ox was a living polyhedron.
In Supergirl (Rebirth), Director Chase doesn't really like or trust aliens, although she's willing to work with them and give them the benefit of the doubt.
On the one hand, Stanhope's teachers and students regard "super-heroically challenged" students as inferior.
Linda: Um... Ms. Bigglestone? Aren't we all equal and stuff? I mean, just because we're not super-powered doesn't meant we should be treated any differently... Teacher: I'm sorry, but no. That is incorrect. Your fate, which I am here to ensure you embrace, is one of mediocrity and fear. As non-super-powered citizens, you may stand back and witness the majesty of your betters. Or, perhaps, become pawns in their super-powered contests. Either way, what you do is of little importance.
The other side of the coin is Lena and her brother Lex Luthor. She hates super-powered beings, especially if they are aliens.
Supergirl: Lena... Lena: All these months... All these months you've been lying to me! Laughing at me! Supergirl: I've never laughed at you. Lena: Liar! You're an alien! A super-powered oppressor! You're the very definiton of evil and you ruined my life! Supergirl: Lena... I'm still me! I'm your best friend! Lena: Not anymore... Not now that I know the truth! You're my enemy now. I have no choice but to destroy you! Supergirl: But why? I'm the same person you've been friends with for months! Why do you have to hate me?! Lena: Because your kind offends the natural order! You float through the sky as if you own it! You change the course of rivers without a thought to the consequences! Your very existence undermines the purity of true human achievement! Superheroes are nothing but a bunch of glory-hogging tyrants, and I will not rest until I see you humiliated and destroyed for what you did to my...!
In an issue of Action Comics, an alternate reality version of Luthor is fighting against a black version of Superman. This Luthor is as white as his mainstream counterpart, and is adamant that he hates Superman as a fantastic racist, and not the normal kind. Simple mistake, he is a bald white guy known for his fanatical hatred of a black guy.
In Elseworld's Finest: Supergirl & Batgirl, Lex Luthor hates aliens. As far as he's concerned, killing a “xeno” isn't murder. Similarly, Batgirl is very bigoted against parahumans (to be fair, though, she didn’t trust normal people either, and at the end of the story she appears to have gotten over her prejudice a bit).
In the H'el on Earth storyline, H'el, a Kryptonian, hates Superboy, a human/Kryptonian clone, with every fiber of his body. This is because Krypton used to use clones as servants until they revolted and nearly wrecked their planet. H'el also thinks Earth and every human on it is inferior to Krypton and Kryptonians. He doesn't care what price Earth has to pay in his goal to ressurect Krypton.
In Superman: Godfall, the Kandorians are incredibly xenophobic and racist against all non-native Kandorians, especially Empireths, who are mutants with psychic powers as well as the typical Kryptonian powers under a yellow sun.
In Swordquest: Waterworld, the air-breathers and the merfolk Aqualanians are on the brink of war. The pirate leader Captain Frost kills a snow-whale and strips it to the bone just to prevent them from possibly siding with the Aqualanians.
There's two levels of this in Tangent Comics regarding the Sea Devils, amphibious fish people. For one, Sea Devils are scorned by humans as freaks, while most Sea Devils consider humans disgusting and barbaric. However, there are dozens of different tribes of Sea Devils (shark people, shrimp people, eel people, etc), and there's quite a bit of racial tension between them as well.
In Tooth and Claw animals that live on the ground are discriminated against by those living in The Seventeen Cities. The reason given by the main character's father is that "The lesser ones serve us as we serve the Gods."
In Alan Moore's miniseries Top 10, robots (or "Ferro-Americans") are second-class citizens. Pete Cheney, one of the main characters in the series, has clear anti-robot sentiments, freely using the term "clicker", which is established as a major slur. When the robotic Joe Pi joins the police squad Cheney belongs to, Pete attempts to put Joe down whenever he can - however, Joe usually wins the resulting battle of wits. In a sequel series, Pete eventually loses his job after an unprovoked assault on Joe. Joe also has to overcome the prejudices of his new partner.
In addition to "clicker", this series also featured another piece of slang regarding robots. At one point, a robot derides Joe Pi as being too human by calling him "spambo". Not only is this a variant on an actual ethnic slur, it's also similar to terms like "coconut" (brown on the outside, white on the inside) and "banana" (yellow on the outside, white on the inside), because Spam is "metal on the outside, meat on the inside".
This is also reversed in the second issue when a robot calls Robyn Slinger aka Toybox "Wetware" - an apparent slur against organic beings.
Jeff Smax is prejudiced against kaiju, because he comes from a fantasy world and made his living as a dragon slayer. He's not about to trust a giant lizard with fiery breath any time soon, is all.
In the prequel story The Forty Niners, anti-robot prejudice is a big part of the plot, as the Skysharks' plot to bomb the robot-populated Tintown district is half of the climax. In the other half of the climax, Steelgauntlet is revealed to be a robot masquerading as a human trapped in a suit of armor in order to avoid prejudice. Only Leni knows his secret, and seems to agree that keeping it under wraps is a good idea.
Other examples of this usually crop up in any of Moore's stories about aliens interacting with humans for the first time, usually referring to humans derogatorily as "chimps" or "apes" and the like. This is especially common in his work from 2000 AD.
The Transformers: All Hail Megatron shows that the universe at large hates the Cybertronians as their war has lead to the destruction of many planets. Decepticons hate organics and any other race they consider back-water.
In The Transformers (IDW) it's shown that Cybertronians weren't above doing this to themselves, with there once being an apartheid depending on how a Cybertronian was born, which by the time the war began had supposedly become a thing of the past.
Transformers: More than Meets the Eye shows that before the war, Cybertron had a caste system depending on what you turned into. Those who turned into industrial alt-modes like mining vehicles were just about the bottom rung, with the only ones lower being the Disposable class, Cybertronians who were so common they were seen as disposable, and had absolutely no rights whatsoever. There was also prejudice against Cybertronians who didn't transform (monoformers, as they're called), and even in the modern day parts of the story, there's still prejudice going around. For example, when Whirl talks about his "nemesis" Killpower, he mentions that he was "ugly as sin", before concluding he was probably a Monoformer and adding that this made it "worse".
Meanwhile, the Galactic Council has marked the Cybertronians as one of the most destructive races, and have refused to let them join. When the Lost Light crew meet one of their ships, the situation starts sour and gets worse from there.
Before this era, Nova Prime sought to expand the Cybertronian empire, and "experiment" on all races he considered inferior to achieve his idea of perfection. Tailgate, for all his innocence, came from this era, and sees no qualms in admitting a military faction he admired killed organic life.
According to Ultimate Fantastic Four, the Chitauri are apparently an outcast caste of the Skrull. Calling a Skrull Chitauri is insulting seeing as they're different.
Warlord of Mars is so filled with racial tensions that almost no people gets along with each other, with the Red Martians in the receiving end of every other race, being treated as source of slave labor and/or nourishment.
The Red and Green Martians were bitter enemies as the two most populous and prominent people in the planet. The Greens were brutal savages who have assaulted the Red's domains and committed appalling atrocities. In the prequel series Warlord of Mars: Dejah Thoris, when a Red Martian tyrant goes on a genocidal rampage against the Green tribes, few people disagree with his actions and fact condone him. Though its shown that genuinely honorable and benevolent do exist such as Tars Tarkas and his daughter Sola, they are treated as exception to the rule than the norm, and the hate against their people is not without justification since they are Always Chaotic Evil. Its wasn't until John Carter arrived on Mars that peace between the two peoples was possible, and even then, it was fragile at best.
The Holy Therns and the First-Born are predisposed to this trope since both of them consider themselves a Master Raceof living gods, and look down on the the Red and Green people as nothing more than animals and savages. They have been at war for eras, so naturally they despise each other as they do people "of lower orders".
The Yellow Martians are a reclusive people that doesn't interact much with the outside world, but its revealed that they too intensely despise the Green Martians, having been nearly driven to extinction by them and forced to retreat to the North pole. Its mentioned that they used to practice slavery, using rebellious Red Martians as bait to hunt beasts.
Not limited to Mars either, the Vathek of Strio, an vampire race of Saturn, has used their neighbors as slaves and blood farms. They are also highly xenophobic towards aliens, treating any Martians as animals and things.
In White Sand, both Darksiders and Daysiders have a ton of predjudice against one another. Darksiders are quick to label the other side barbarians and don't seem interested in learning their culture, whereas Daysiders, especially Sand Masters, believe that Darksider ancestry poisons the bloodline irreparably.
X-Men. Hands down the Trope Codifier, where anti-mutant sentiment is used as a metaphor for racism (and homophobia), complete with their own slurs like 'Mutie', which is essentially the mutant equivalent of the N-word. Especially blatant in the second movie:
Iceman's Mom: Have you tried... not being a mutant?
It actually gets worse in Ultimate Marvel as mutants are something of a legal anomaly (genetic modification is illegal, yet mutants are born this way) and in recent comics have actually been forced to wear power suppressors or live in reservations; even before that, it was actually a crime for mutants to use their powers, even in self defence, after Magneto attacked New York. In the mainstream universe, mutants are often depicted as living in slums or ghettos, such as District X in NYC (in the Ultimate universe, this is replaced with real life Harlem) or even the sewers, and mutant hate crimes is somewhat common.
It got even worse during the "Divided We Fall"/"United We Stand" storyline when it stood revealed that mutants were actually created by the US Government trying to recreate the Super Soldier formula: not only were Nimrod-type Sentinels unleashed to wipe them out, the US started to fracture because of it.
The obvious metaphor was parodied in an issue of X-Force, where Anarchist, an Afro-Canadian mutant, described being a mutant as being "Black with a little black added".
Superman: I am not an "Anti-Mutite." Wolverine: Sure you are, next you'll be sayin' we should have our own school! Superman: You do have your own school!
The bulk of the hate against mutants tends to stem from two factors: the fact mutants are supposedly the natural evolutionary replacement for humans, thus making people fear mutants will replace humans, and because many mutants have powers that could be used to either harm humans or commit crimes, leading to bigotry against even mutants who don't have active powers, beyond physical mutations or defensive and passive abilities (which the majority of the mutant population in-universe has).
There's also Magneto, who goes so far as to give Mutants the egregiously biology-failingspecies name of Homo Superior. There are so many things wrong with that it could be its own article. Ironically, his foes, the X-Men, have taken up this idea as well (along with Magneto himself) and are now just as prone to asserting that mutants are a separate "species" from regular humans, even though a solid majority of mutants are actually born to human parents and are themselves still capable of interbreeding with other humans. This is a massive case of Genre Blindness, since not only do normal humans tend to treat mutants as if they were a different species altogether, most mutants actually agree with them! Hence their ongoing PR problem.
Well technically speaking the Domesticated Dog is a separate species evolve from Gray Wolves but they can interbreed and are genetically identical, with only a less than 1% difference. So technically speaking its not suppose to be homo superior but homo sapiens superior, as mutants are not a different species but a sub-species.
On the flip side of this, many mutants see themselves as superior to humans because of their abilities and so often have anti-human prejudices, which are usually exasperated and made worse thanks to the anti-mutant bigots ruining their view of humanity.
House of M flips the script by showcasing an Alternate Universe where mutants are the dominant species and humans are the ones held down and oppressed. Driving the parallel home, it's established that Sam Wilson is considered the "token human" of the otherwise mutant NYPD, and Luke Cage mockingly claims that Wilson is only kept around for diversity.
The U-Men are a weird example, as they don't so much hate mutants as envy their powers, and so figure they "deserve" the opportunity to vivisect mutants and transplant their organs in pursuit of upgrading themselves.
Perhaps the most terrifying thing about anti-Mutant sentiment in the Marvelverse is how easily it seems to reach ethnic cleansing levels of intensity. It has been repeatedly shown in Marvel, as early as God Loves, Man Kills, that many anti-mutant members, particularly those like the Purifiers or the U-Men, are willing to murdermutant children for the "sin" of being mutants. There's a reason why, in Schism, most of the students prefer to stay with Cyclops and learn how to fight, because, as their spokesperson notes, they live in a world where they went from "civilian" to "target" the moment their X-gene activated, so they had best learn to fight back.
Interestingly, there was an issue of What If? where Magneto created an actual utopia for mutants and two mutant parents, Rusty and Skids, gave birth to a child whose X-Gene was active automatically and also could change their powers on the fly, being the first so-called "homo ultima". This frightens Magneto's Acolytes so badly of being in the same position as they put humans that they went and killed the child. The Irony was not lost in those who were furious at their actions. This message was kind of ruined by the twist, though, in which it was revealed that there was no "homo ultima", the child was a perfectly ordinary baby that Magneto tricked his followers into thinking was a fictional next step being because apparently getting them to agree to an Enemy Mine scenario was the only way he could think of to solve what ultimately was a situation caused by his own weak leadership.
Alex + Ada has sentient A.I., who a generally met with outright hostility by society. Once, an android went to a concert by itself, without it's owner, and people lost their shit and destroyed the poor thing.
PS238 shows several (rather worrying) cracks in human-metahuman relations. On one side we have things like Ultima and Sovereign Powers saying things like solving the world's problems is a purely metahuman business and actively discrediting Badass Normal vigilantes like The Revenant. On the other side we have things like metahumans (or at least ones with mental powers) being forbidden from serving in government or in the army if they have a secret superhero identity, the original Project Rainmaker and argonite made by the baselines. And then we have things like metahuman discrimination against the F.I.S.Ss for being the 'common and unremarkable' power-set with F.I.S.S being referred to by their 'number', Praetorian Academy, and what happened to Argos...
When Wonder Woman and Superman started dating in the New 52, they end up crossing paths with the Olympian Gods (who in this continuity are Wonder Woman's biological family, as Zeus is her father). They express disgust that she is dating a being who is neither a God nor a human, and talk to Superman like he is an animal. However, after Superman kicks Apollo's ass, Strife changes her stance and starts swooning.
In the New 52, it turns out Harvest's true motive is aligned to this. He gathered superpowered teens and made them kill each other until only "the strongest" remain...and yet, doesn't seem to value the resulting "Ravagers" too highly either. This, turns out, is because Harvest hates all meta-humans. His son was killed by meta-humans, so the crux of his plan seems to be making ultra-violent meta-human youth, sending them out into the world and then getting them all purged.
While not showcased nearly as much as anti-mutant sentiment, Marvelverse citizens also hate and fear androids like The Vision, usually with the same (or similar) Darwinian justifications. In an ironic inversion of the usual anti-mutant line, one anti-robot fanatic denounced Vision as Not Even Human, while accepting the Scarlet Witch as one.