Snakes (ophidiophobia), Reptiles (herpetophobia)
- The Spelunker from Spelunky, being kind of an Indiana Jones expy hates snakes, too. Doesn't really seem to stop him, though.
- World of Warcraft has a shout out in the form of an NPC with a strong fear of snakes who's named Harrison Jones, which takes Indiana Jones's last name and his actor's first name.
- The last line of a journal entry in Vesuvia that mentions the discovery of a charred snakeskin is "Snakes - anything but snakes..."
- Gemini Man from Mega Man 3 hates snakes. Not surprisingly, he takes massive damage from Snake Man's Search Snakes.
- Part of a certain side quest chain in The Lord of the Rings Online involves retrieving some baby turtles from the work shed of a hobbit named Grobo Dogroot who happens to be deathly afraid of turtles. When you go to pick them up, each and every one is called "Grobo's Greatest Fear."
- In LEGO Indiana Jones, several puzzles revolve around Indy's fear of snakes. You have to get rid of the snakes with another character (and it's not as easy as attacking them, since they're often in deadly mud) so Indy will join you where his skills are needed.
- The Bishop of Southwark in Fallen London, who asks you to bring him deadly beasts to breed an Evil Detecting "Hound of Heaven", repeatedly reminds you "no serpents!" Naturally, the Hound turns out to be just that — a huge white snake with a devil-detecting gaze.
- Rikku from Final Fantasy X-2 freaks out when fighting the Battlesnakes screaming "Snake! Snake?! Snaaaaaaake!!!". Strangely Riku has no problem with the anaconda in Final Fantasy X despite them being far more terrifying than the Battlesnakes.
- In Diablo 2 when the Druid enters the Claw Viper Temple, he mentions he hates snakes.
- The Shieldbreaker from the Shieldbreaker DLC of Darkest Dungeon, though her fighting style is based on snakes, is absolutely terrified of them due to a traumatic encounter with one during her escape from a wagon bound for a horrible vizier that she was being sold to, which ended with her having to cut off her hand to halt the spread of its venom and free herself from the wagon. On several occasions upon camping, she has the chance to have a nightmare about giant deadly snakes, which throws her immediately into Horror mode and draws any other heroes with her into it for the battle of their lives.
- Assassin's Creed Origins: Bayek has a severe dislike of snakes, even quoting the Trope Namer in one quest. Understandable, since regardless of how strong Bayek is, those scaly bastards will take off an entire bar of his health in a single bite.
- Daxter: This exact line is uttered by the namesake Ottsel after he wakes up from his Indiana Jones-themed dream, which to say the least, included no shortage of serpents for him to take care of.
- Ryoh from Warbears, to the point where he climbs out of a window and across a ledge, then through another window to avoid a spider.
- Ryu of Street Fighter, after waking up with a spider in his mouth once, has an intense dislike of spiders. He even lampshades it when fighting Spider-Man in Marvel vs. Capcom 3Spiders... I hate spiders.
- Ryo Sakazaki from Art of Fighting and The King of Fighters. It was a prank from his friend Robert (putting a spider in his mouth while he was sleeping) that caused it.
- From Resident Evil, Claire Redfield has no problems gunning down zombies by the truckload. She dislikes spiders. Especially those seen in Raccoon City and Rockford Island.
- Artur from Fire Emblem: The Sacred Stones. His best friend Lute once tried to help him... by placing spiders on his face when he was sleeping. Yep, Lute is special.
- Apparently Matt "Positron" Miller, current lead developer of City of Heroes, is afraid of spiders in addition to clowns (see below). When half of the game is jam-packed with them, you gotta wonder...
- Various spirits from Ghost Master specialize in exploiting certain fears; one of them in a giant spider.
- One of the quests that you can do in Stormreach Harbor in Dungeons & Dragons Online involves a guy named Berne Jorn who's been afraid of spiders ever since he was a kid. The quest he sends you on, which is called "Arachnophobia," has you clearing the eight-legged bastards (including a huge boss-level one) out of his family crypt.
- Pokémon Black and White have Joltik and Galvantula◊, who have Unnerve as one of their abilities. Said ability makes the opponent afraid and unable to use berries. How Joltik has this is anyone's guess.
- Toonstruck's Drew Blank exclaims "Spiders! Why did it have to be spiders?" upon seeing a couple of them crawling on the wall.
- Bounder Boffin of The Lord of the Rings Online is terrified of spiders, which you have to kill during the introductory instance for Hobbits in order to help him cut through Old Odo's Leaf-farm to escape a Black Rider.
- Farkas, an otherwise fearless warrior of Jorrvaskr in The Elder Scrolls V: Skyrim, at one point refuses to go any further in the Tomb of Ysgramor after encountering giant spiders there due to his experience with them back in Dustman's Cairn.
- Mass Effect:
"If I never see another spider again, I'll die a contented turian. Unless they have spiders in the afterlife. Damn."
- Tali is apparently afraid of spiders, judging by her reaction to the Gestation Pods hatching if you should take her along on Grunt's mission in Mass Effect 3.
- Garrus also dislikes spiders, though to a lesser extent.
- Wilson from Don't Starve hates spiders.
- Kormac from Diablo III does not like spiders. At all.
- Petra from Minecraft: Story Mode apparently has a thing against cave spiders, even referencing the Trope Namer. She takes on normal spiders earlier in the game with no hassle, though."Cave spiders. Why'd it have to be cave spiders?"
- Adelbert Steiner in Final Fantasy IX, sort of. He's deathly afraid of oglops, an otherwise harmless insect. So is Blank, though not to the same degree (he says he "can't stand them", but is able to put up with them for the sake of the plan to kidnap the princess). Though when Blank's armour breaks and the oglops are released, both Steiner and Blank begin running around in a panic. Garnet/Dagger later fakes a fear of oglops in order to make her "ordinary girl" act more convincing.
- Steiner even punches Regent Cid clear across the room and begins ranting ("Get that repulsive bug off the throne and call the Regent!") when he first reveals himself to the party, having been cursed with an Oglop body.
- Fiona from Haunting Ground is terrified of insects, when she kicks open a wall to get the item and dozens of bugs come out, Fiona is less than thrilled.
- Kick Chick Chie Satonaka from Persona 4 will happily take on all kinds shadow demons and murderers, but little bugs? Count her the hell out◊.
- Blathers the Owl from Animal Crossing hates bugs of all sorts, as made obvious by how he reacts every time you turn in something for the museum's bug collection.
- Lyle Smithsonian of Metroid: Other M really hates bugs. Guess what's invaded the Bottle Ship?
- Fire Emblem:
- Florina from Fire Emblem: The Blazing Blade is terrified by bugs (a support conversation shows her panicking when a bee flies around her), among a few other things.
- Fire Emblem Fates also has Ignatius, who has a handful of fears (like clowns and ghosts), but insects are his biggest fear according to many of his support conversations.
- Leonie from Fire Emblem: Three Houses can't stand to even look at spiders, centipedes, or other creepy-crawlies. In her supports with Shamir, Shamir uses this fear as a tool to help Leonie improve her archery skills.
- Ashley from Until Dawn hates bugs, and will freak out when she sees them crawling on the objects she just picked up.
- Karol in Tales of Vesperia is shown to be petrified of them when the party visits a forest teeming with insects. In a rare show of kindness, Rita gives him a can of bug spray, which becomes a skill called 'Bug Busters' for him.
- In the Resident Evil 2 (Remake) when exploring morgue there's a drawer crawling with huge cockroaches. Leon gives a startled yell when he pulls the draw out but is otherwise fine, but in Claire's scenario, she cries out loudly and makes noises of disgust at the sight of them.
- Noel Vermillion from BlazBlue is afraid of bugs, especially ones with lots of legs. Keep in mind she's only five, even if she doesn't look like it. When one considers Arakune uses them in his attacks, her battles with him are... an experience.
- The eponymous Pikmin flee in terror from otherwise harmless Mitites.
- Grendel in Labyrinths of the World 4: Stonehenge Legend is afraid of bees.
- In The Vagrant, before and after the boss fight with the Ground Shaker, Vivian rants about how much she hates bugs.
Mice and Rats (musophobia)
- The Good Fairy in Ceville. Obviously, you have to exploit her weakness to solve a puzzle.
- Zelda from The Legend of Zelda: Spirit Tracks doesn't like mice. Used as a gameplay mechanic, as Link has to get rid of those rodents before she will move on. Understandably it comes up as the third part of the final boss fight where if she gets touched by one, she fall under Cole's control. This creates the amusing sight of an imposing suit of Animated Armor (which Zelda possesses) shivering in fear at the sight of a mouse.
- The title character in Nick Chase and the Deadly Diamonds announces at one point that rats are his one weakness, his Achilles' heel.
- Monokuma and Monomi in Super Danganronpa 2 both reveal that they hate mice when the player approaches Nezumi Castle on the fourth island (which isn't supposed to resemble any castle from the Disney Theme Parks, honest!). As such, they can't even go near it. This turns out to be plot-relevant. Because Jabberwock Island is all a Virtual Reality simulation, the Future Foundation, the creators of it, decided to implement a failsafe if it all went pear-shaped. Anyone in the teacher role is made to be scared of mice so that they can't go anywhere near the castle, which contains the code to access the inside of the ruins, where the means of activating the Forced Shutdown lies.
- Metal Gear: Naked Snake has a fear of bats, and (by extension?) Dracula.
- Mr. Driller: Ataru is deadly afraid of bats, especially vampires.
- Serge from Chrono Cross was said to have this (though he's apparently grown out of it by the time the player controls him). Justified in that he was attacked and nearly killed by a panther demon as a small child. We learn later that Serge's father, Wazuki, was turned into a cat-like form by FATE because that was the thing that Serge feared the most.
- Creepers in Minecraft flee from cats and ocelots.
- Ushnar gro-Shadborgob in The Elder Scrolls IV: Oblivion: Shivering Isles. He provides a quest of getting rid of a Khajiit beggar (which is obviously unavailable to Khajiit PCs). Even moreso on how he comments on the current events based on the stage(s) of the main quest, thinking that cats and Khajiit are the root of the problems.
- Celine from Asdivine Hearts absolutely adores domesticated animals but is also deathly afraid of them due to being attacked by a dog when she was a child. This is revealed in the game when the talking cat in the party gives Celine permission to pet him and approaches, only to be thrown into the wall by her reaction. She compensates for this fear by having a large collection of stuffed animals instead.
- A short time into the events of Geist, it is revealed that Big Bad Volks's Dragon Rourke is afraid of dogs. Close to the end of the game, Volks holds a meeting behind locked doors and gives specific orders to shoot anyone who comes close who isn't himself or Rourke. The solution is straightforward: possess Rourke. To possess someone, you must first terrify him. Thus, you undergo a series of short missions for the sole purpose of getting a dog into the same room as him.
- Alessa Gilespe from Silent Hill was terrified of dogs, which due to her and the town itself being a Reality Warper who brings fears and abstract concepts to "life" is responsible for several monsters you see throughout the series; Split Head, Groaner, and possibly the Caliban.
- According to the Drama CD of Guilty Gear XX, Zappa is terrified of dogs (then again, he seems to be scared of everything). Guess what? One of the ghosts possessing him takes the form of a huge, hulking black dog.
- Frederick from Fire Emblem Awakening is afraid of wolves due to nearly getting killed by one when he was younger. Even something that looks like a wolf, like a taguel, can trigger this.
- Tron Bonne, from Mega Man Legends, is afraid of dogs and was once chased up a street lamp by a dog.
- Marcus Fenix from Gears of War received his trademark facial scars from being mauled by guard dogs in prison, and has been nervous around them ever since.
- Daruk from The Legend of Zelda: Breath of the Wild has been afraid of dogs ever since they were a child. Zelda finds this very amusing.
Frogs & Toads (batrachophobia)
- Lucca of Chrono Trigger. Becomes awkward when it comes up immediately after they meet with one of the party members, a giant anthropomorphic frog.
- Refia of the 3D versions of Final Fantasy III has a fear of frogs, which makes for a fairly amusing conversation the two times where you have to transform into one to enter a dungeon. It's even better if she is the character who has to cast the "Toad" magic.
- Volgin from Metal Gear Solid 3. The phobia is so strong that if you toss a live frog at him during your boss fight with him, he'll stop attacking you to kill the frog, allowing you to get a hit in.
- Cornet of Rhapsody: A Musical Adventure suffers from this. Unfortunately, frogs are hiding in every other container in the Marl Kingdom. Oh, and there's a kingdom of bipedal, sentient frogs.
- In The Legend of Zelda: Twilight Princess, Midna is very grossed out by frogs and toads, to the point that she refuses to give you any hints when fighting the Deku Toad miniboss in Lakebed Temple.
Slugs & Snails (molluscophobia)
- Ursula of Breath of Fire IV is utterly terrified of sea lice (a harmless bug). Especially hilarious as this ends up being revealed in a "What Do They Fear?" Episode segment between her and Princess Nina, and Ursula is normally a Type A Tsundere who tries to be tougher than most men...
- Carol Palecki in Mitsumete Knight. It's one of the rare things that makes her lose her permanent Genki Girl attitude or rather, her permanent Genki Girl façade. Do not pull a prank of putting a slug on her, or she'll immediately cut all ties with you.
- Shale loathes birds in Dragon Age: Origins due to its stint as a statue in Honnleath. as a prank you can give her an unsquishable pigeon and force her to wear it instead of armour, all the time with the Feast Day DLC.
- Mike from Until Dawn hates birds calling them "rats with wings" after one bird startles him to the amusement of his girlfriend Jessica.
- Portal 2:
GLaDOS: AAGH! BIRD! BIRD! KILL IT! It's evil!
- GLaDOS comes to hate them. During her stint as a potato, one picked her up against her will, escorted her to its nest and started pecking at her, so she has good reason to be distrustful.
Wheatley: AAH! BIRD, BIRD, BIRD, BIRD!
- Wheatley also demonstrates a dislike for birds after he's attacked by one (perhaps even the same one GLaDOS had a run-in with). To be fair, he did break its eggs.
Flying (aviophobia) or Heights (acrophobia)
- All playable lawyers, save Mia Fey and Athena Cykes seem to suffer from this in the Ace Attorney series: Miles Edgeworth (who already has a Seismophobia to boot) needs Gumshoe to fetch him books from the higher up shelves, Phoenix Wright has to be led by his hand by his teenage sidekick when passing a bridge and breaks out into hysterical catchphrase-shouting upon boarding a Ferris Wheel and Apollo Justice can't ascend as much as 10 meters without starting to shiver like a dry pile of leaves.
- Alister, Lara Croft's Non-Action Guy partner from the Tomb Raider series, does not like heights. At all. They make him "positively nauseous," as he comments at one point in the Japan mission of Tomb Raider Legend where Lara is making a dangerous climb up a really tall office building.
- Blaze the Cat from the Sonic Rush series is often implied to have a fear of heights, especially when they reach Sky Babylon.
- Emma, Hal's sister in Metal Gear Solid 2 doesn't like heights when asked about it by Raiden, but stated it's preferable to Water.
- Bartz Klauser in Final Fantasy V has a fear of heights ever since he almost fell down from the roof of a two story house while playing hide and go seek. He reveals this the first time the party rides the wind drake, and Galuf physically hurls him onto its back. Later on, he hesitates before jumping off the relatively low height of Bal's drawbridge into the moat.
- As part of its many Call Backs to earlier Final Fantasy games, Vivi Orunitia from Final Fantasy IX, just like Bartz, has a fear of heights stemming from falling from a great height when he was young (specifically falling out of the cargo ship.)
- Chrono Trigger has the example of Golem Boss who, after Dalton summons on top of the wing of an airship, cowers in fear from the height, without attacking. If not killed quickly, he then runs away.
- Deacon of Fallout 4. He's very apprehensive about getting in a vertibird, and finding the wreck of a pre-war plane leaves him cringing at the thought of flying that high.
- In one mission in Grand Theft Auto IV, Niko seems nervous about having to take a lift on the outside of a building to get to its roof. And in San Andreas, Cesar refuses to get into a crane because he's afraid of heights.
- Leo in A Way Out fell out of a tree when he was eight and has had trouble with heights ever since. As a result, whenever there's a choice involving heights (going over or under a bridge, skydiving vs walking through a jungle, etc), he'll always prefer the option that requires him to be near ledges as little as possible. It even affects his side of the screen, as his depth perception gets distorted the further off the ground he gets.
- Margaret in Rune Factory 4 is terrified of heights. Ironically, her house exits out onto a wooden boardwalk bordering a cliff. In one event, she trips on the boardwalk and remains where she is for a time because she was too afraid to move.
- Sonic the Hedgehog displays a fear of water in some adaptations (such as Sonic X, for instance), though not actually in the Modern games.
- Ramses III has a good reason why he is afraid of Water
- Raine Sage, Tales of Symphonia. An optional skit reveals that this is because when she was young and she and her family were being chased, she fell from a boat and nearly drowned.
- Curly Brace in Blade Strangers due to being a Robot Girl and almost drowning in the Labyrinth in Cave Story she hates water. She even has Nightmare Sequence about drowning.
- Raz from Psychonauts, because of a family curse.
- Metal Gear Solid: Emma Emmerich is terrified of water thanks to a Childhood Trauma. Ironically, Hal stated she used to swim like a fish and it's hinted she could still do that.
- Ayako Katagiri in Tokimeki Memorial. A fear very well known in the series' fandom, and milked for all its worth by the creators, as antics-wise, she's regularly paired with Nozomi Kiyokawa, the resident swimming-lover and champion (who, ironically, suffers from a primal fear of her own, thunder).
- Lesley Lopicana in Mitsumete Knight, a Spiritual Successor of Tokimeki Memorial. She's an Expy of Ayako, but unlike her where the origins of her fear were never explained, we get to know how Lesley got this fear of water (long short story - that you can read in the game's Character Sheet, - it's due to a Childhood Trauma).
- The Dahaka from Prince of Persia: Warrior Within. There's even an alternate ending where you kill it with the Water Sword. Also, any sand monster in this game loathes water. Strangely, the ones in the prequel can be fought in ponds.
- Chloe Valens from Tales of Legendia.
- CJ from Grand Theft Auto: San Andreas claims to be afraid of water at one point, after getting a discarded condom on his face while swimming as a child. Ironically, he's the first character in GTA not to suffer from Super Drowning Skills.
- John Marston couldnt swim in Red Dead Redemption so you wouldnt go places before the game allowed you to. Come the prequel,Red Dead Redemption II , hes terrified of water and thats why he cant swim. He constantly gets teased about it. If hes near a body of water, he can be heard breathing much heavier.
- Rydia's fear of fire can be chalked up to Cecil and Kain's delivery burning the village of Mist to the ground in Final Fantasy IV. Very soon after, she's forced to confront this fear and cast fire magic to melt a wall of ice blocking the party's path to Fabul, as she is the only one capable of doing so.
- The dragon in Loom is afraid of fire, a fact Bobbin uses against her with either the Terror or Sleep draft to set her hoard — transformed by him from gold into straw — ablaze.
- It's hinted that Milla Vodello of Psychonauts is a pyrophobe due to the orphanage where she worked burning down with the children inside it.
- Heather in Silent Hill 3 is afraid of fire. She comments that "it's scary somehow..."
- Alessa has a fear of fire for a very similar reason.
Other nature phobias
- One of the player characters, Rikku from Final Fantasy X has a phobia of lightning (astraphobia), which she gets over in the sequel by camping in an area in Spira where lightning is striking down nonstop.
- Tails of Sonic the Hedgehog also has astraphobia. He first displayed this in Sonic the Hedgehog: The Movie, but wasn't displayed in the games until Sonic Mania Plus.
- Earthquakes (seismophobia) — Miles Edgeworth from Phoenix Wright: Ace Attorney. The first major crack we see in Edgeworth's stoic facade is that he turns into an absolute mess at the slightest of tremors. It's no better in Trials and Tribulations, when he passes out after an earthquake hits Hazakurain. It also extends to airplane turbulence (which can resemble tremors) and elevators. Justified in it being the result of a traumatic and tragic incident he experienced as a kid.
- Jonathan Ingram in Policenauts is a cosmophobe by his own admission, and also appears to show some level of claustrophobia. This clearly doesn't work in his favor when he has to leave the Moon via a material transport relay. Depending on the players' responses to Ed, and how long it takes the player to make the decision to leave, it will extend the action sequence. The first time you beg Jonathan to enter the pod, he will refuse.
- Timbersaw from Dota 2 has a severe fear of trees, to the point that he built a mechanized suit for the purpose of cutting them down.
- Barry Dejay in Backyard Sports. He plays worse on the Bling-Bling Brothers Circus in Backyard Basketball just because he is afraid of clowns.
- The players of City of Heroes often ask for a Clowns powerset for the Mastermind (pet summing class based on minion-commanding villains), but are denied because Matt "Positron" Miller, the lead developer, is afraid of clowns.
- Nathan Drake from the Uncharted series. At the end of Uncharted 2: Among Thieves, Elena asks him on a scale of 1 to 10 how scared he was that she would die, he gives it a 3 or 4. Guess what was at 10?
- Trevor Philips from Grand Theft Auto V hates clowns, which unfortunately are what he sees after sampling someone's marijuana.
- Sexy Women (venustaphobia) — Laharl from Disgaea He becomes a beautiful woman in D2.
- Lon'qu from Fire Emblem Awakening, which stems from his guilt of feeling responsible for the death of a childhood friend. He'll eventually make an exception for whichever female you decide to pair him with (and his daughter, should he have one).
- Guy from Tales of the Abyss, due to a VERY traumatic event in his childhood.
- Super Mario Bros.:
- Luigi is afraid of a lot of things, but most of all, he's deathly afraid of ghosts, Boos especially. Despite this, he has to fight hordes of them in Luigi's Mansion to save his brother, Mario. He finally, if only mostly, overcomes this fear at the end of Luigi's Mansion: Dark Moon, even going so far as to adopt the Polterpup as a pet.
- Yoshi is afraid of ghost houses, so he stays out of them while Mario and Luigi explore them. In spite of this, two bosses in Yoshi's Island and one in the remake are ghosts. Also in both games, one Yoshi's relay leg consists entirely of fortresses while another has all castles.
- Yukari Takeba from Persona 3 is also afraid of ghosts.
- When Roxis was still a freshman during the early parts of Mana Khemia Alchemists Of Alrevis, he was, er, traumatized (he was foaming at the mouth!) by Pamela, the school's resident Cute Ghost Girl. Since then, he would have a hard time searching for items anywhere that could possibly be haunted (ranked as Super Hard for him), which, incidentally, are ranked Super Easy for Pamela.
- Luso from Final Fantasy Tactics A2 revealed his fear of ghosts when the clan must defeat a group of Undead. Adelle teased him afterwards.
- Youmu Konpaku from Touhou is scared of ghosts — which is ironic, because she just happens to be half-ghost herself, and has a Cute Ghost Girl as a mistress.
- Tear Grants from Tales of the Abyss is scared of ghosts despite being a Kuudere.
- Tales of Vesperia: Rita Mordio really hates ghost-ships.
- Metal Gear Solid 3: Snake Eater: Naked Snake is terrified of anything involving the undead. Bats make him think of Dracula, and merely mentioning Dracula is enough to give him nightmares. Because Hideo Kojima loves to screw with his own character's minds, Naked Snake gets to face the ghosts of every person he's ever killed in the game. It's a little unsettling for us, the players, but it's horrific for him. In Peace Walker, there are more ghosts in some bonus levels. When Chico, a fan of cryptozoology, starts describing an optional boss as an "undead dinosaur" brought back to life by Haitian zombie-makers, Snake's phobias kick right back in and he starts trying to rationalize it as just an "ordinary" dinosaur that happens to be skeletal and immune to conventional weapons.
- Ragna the Bloodedge's Joke Ending in BlazBlue: Continuum Shift reveals that he is terrified of ghosts. So his joke ending turns him and most of the cast into ghosts. It's canon too; he is freaked out by Sena, one of the personalities that make up Platinum the Trinity, when Sena threatens to haunt him for the rest of his life in an attempt to mooch a meal off of Ragna. To top it all off, the true form of the Big Bad Terumi is a creepy grinning green ghost.
- Princess Pitts in Chibi-Robo! possesses a lady-like terror of monsters and the like. As Chibi-Robo, you can use a Ghost suit to help train her to overcome her fear, though it takes a while and she faints a couple times initially.
- Knuckles the Echidna of Sonic the Hedgehog was revealed to have this in Sonic Adventure 2, but he managed to overcome it by fighting and defeating the king of ghosts, so he doesn't mind them anymore in latter games.
- Chip from Sonic Unleashed, as seen in the short Night of the Werehog.
- Judging from what she says about the Old Chateau (a place where Ghost Pokemon and actual ghosts lurk), Gardenia, the Eterna City Gym Leader from Pokémon Diamond and Pearl has this phobia. (Oddly enough, if you challenge her with actual Ghost Pokemon on your team, it doesn't make any difference.)
- Hometown Story has its physically extremely strong female blacksmith be afraid of ghosts.
- Ringo Andou from Puyo Puyo is REALLY scared of ghosts. The mere sight of Yu and Rei (who are harmless and just like having fun with quizzes and puns) is enough to have her scream in terror. In an ironic twist, she discloses that she's into paranormal phenomenons.
- Elie MacDowell and Millium Orion in the Kiseki Series hate ghosts and do not want to be near them whatsoever. Though to be fair to them, when ghosts can and will kill you as they do in this series, there's a really good reason to be afraid of them.
- Fate/Grand Order: King Leonidas of Sparta can take anything that has a shape, ranging from men to even dragons. But he's scared shitless of ghosts that when he went to rescue his comrades from a haunted apartment, he was instead surrounded by ghosts and his fear took over him that he looked like he's been possessed by his (non-existant) inner dark side. This is the same Leonidas that said this to his men during the Battle of Thermopylae, "TONIGHT! WE DINE! IN HELL!!" by the way.
- Seiji from Spirit Hunter: NG is terrified of the supernatural, to the point that just hearing about them causes him to seize up in a way similar to an allergic reaction. Unfortunately for him, he's a main character in a horror adventure game.
- Tifa in Final Fantasy VII Remake is shown to be afraid of ghosts when the party visits the Train Graveyard (in the original game, it was just a short level but in the remake, it's a full chapter). Aerith even beckons Tifa to get behind her and hold her for comfort.
- Alan Wake: Alice has a crippling fear of the dark. And don't tell me you didn't flip on a few lights yourself after/while playing through the game.
- Daniel from Amnesia: The Dark Descent has a bad fear of the dark after an incident from his childhood. Staying in the dark too long makes his sanity lower and causes hallucinations, blurred vision, and teeth grinding. Too bad they didn't have very good lighting in 1839.
- Wolfgang from Don't Starve is afraid of the dark, which causes his Sanity Meter to drop faster during the night.
- Nobody in LEGO The Lord of the Rings can go into dark places without some light source; they back out shaking their head. This gets downright silly when you consider that Dwarves typically live underground, and that Gollum is very well-adjusted to darkness and light actually hurts him. They should be fine in the dark, but no. You have to send Frodo (who carries a light) into a dark cave first so that Gollum can go in and climb up the wall that starts there.
- Hayato in Fire Emblem Fates tries to act mature and Wise Beyond His Years and hates being treated like a kid, but a fear of dark places is his weak point. The Boo Camp DLC (fighting Faceless monsters on a dark mountain) even has him in tears during his pre-battle quote.
- Porcelain (porcophobia?) — Guybrush Threepwood. Speculated to have been caused by being hit over the head with a porcelain vase in the first game. The developers have said they added this just as a gag - after all, who is scared of porcelain? Referenced in Tales of Monkey Island Episode 1: Launch Of The Screaming Narwhal, when you have to pick up a porcelain action figure. Guybrush grits his teeth and reassures himself "Calm down, Guybrush, it's only a little porcelain..."
- AGAIN Emma Emmerich shows up on this list: she doesn't like sea lice at all. We also have Big Boss himself, scared of vampires and zombies. This is a subversion in terms of the 'recurring obstacle' trope - vampires are in the series (in a form, anyway), but Big Boss never encounters one.
- Bald people: May of Guilty Gear has an extreme fear of bald men, and can even sense when someone is bald, as shown during the Story Mode in XX when she runs into Dr. Faust (who, under the paper bag, is bald).
- Battler Ushiromiya is terrified of any vehicle that shakes when it moves, as was his late mother Asumu.
- Flora, Layton's ward in the Professor Layton games, is afraid of being left alone (monophobia).
- Artix, normally fearless paladin extraordinaire in AdventureQuest Worlds, is utterly terrified of the color pink (which Beleen mercilessly teases him about).
- Florina from Fire Emblem 7 isn't only afraid of insects, but is terrified by bows (justified, because as a flying unit, she is vulnerable to them) and suffers from a mild case of androphobia.
- All dwarves in Dragon Age (apart from those born on the surface, obviously) tend to have some fear of the sky (possibly Agoraphobia or Ouranophobia) due to the vast majority of them living in underground cities. They fear that going to the surface will not only make them lose their 'stone sense', but that they will fall up into the sky (this is called Casadastraphobia). Of the three dwarves you can recruit, one is a surfacer anyway, and the other two overcome their discomfort fairly quickly. Anders the mage appears to have claustrophobia, given his comments whenever you venture to the Deep Roads in Dragon Age: Origins Awakening and Dragon Age II. There are also plenty of people who are terrified of mages/magic/demons, and of those, plenty are justified.
- In Ib, Garry is utterly freaked out by all the blue dolls. Can't blame him considering one of them stalked him down a hallway and there was another time where a whole bunch of them captured him and forced him to play a game with them, but he found them disturbing even before any of them did anything.
- In addition to fearing sexy women (see above), Laharl is also horrified by declarations of love and positive thinking (claiming that "Eternal Love" is the worst of all. He's mostly over it by the end of the game.
- Parodied in Deadfall Adventures, where James Lee Quatermain's nonhuman archnemesis is... math. Naturally, he comes across not one, but two puzzles involving math — in the Mayan numeral system, no less.
- According to Mordin Solus in Mass Effect 3, Urdnot Wrex, krogan badass and leader of his people, is Afraid of Needles.
- The Rattled ability introduced in Pokémon Black and White likely runs off of this trope, since the attack types that activate it—bug, dark, and ghost—are common phobias.
- After reaching the Empty Room in Maze: Subject 360 the villain appears out of nowhere and asks which is the main character's greatest fear. You get to pick from a list which consists of nyctophobia, claustrophobia and fear of injury.
- In Baldur's Gate II, the elf Aerie is claustrophobic. When the party finds that the Big Bad has fled through a magical portal, one character speculates may very well lead into the Underdark, an underground world evil enough to compete with hell itself. If Aerie overhears this, she immediately freaks and makes it very clear that she doesn't want to go there. Guess where the whole of the next chapter takes place...?
- Evolve: Bucket seems to suffer from chapodiphobia (fear of octopuses), judging by how utterly terrified he is by the Kraken, the only monster to get such a reaction from him:Kraken engaged! NOT LOOKING FORWARD TO THIS!