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Sonic himself looks little like his animal namesake. His spikes look more like styled hair and he hardly has a snout. Instead, he has a jellybean-like nose that's close to face. Same goes with Amy, Shadow, and Silver who are also hedgehogs. Also, hedgehogs aren't blue, pink, black, or silver.
Knuckles is an echidna, but because his spikes look more like styled hair, he hardly has a snout, and has a jellybean like nose that's close to face, it wouldn't be too hard to mistake him for a "hedgehog".
And they're not even closely related. Echidnas are as closely related to humans as they are to hedgehogs (they're actually related to the platypus).
Nack the Weasel doesn't even look like a weasel.
Espio the Chameleon looks like a purple rhino more than he does a lizard.
Hell, several of the characters hardly resemble the animals that they're supposed to be. Only a few are actually readily identifiable as the species they're supposed to be. Tails is the one who looks most like his species; with Cream, Vanilla, and Vector also being easy to tell. Everyone else, though...
Chuchu from Kirbys Dreamland 3 is supposed to be an octopus, but looks more like a squid, or ghost, or...something.
It's because she's a flapjack octopus, but even then...
Tiny the Tiger looks like some kind of big cat, but definitely not a tiger. He apparently was originally intended to be a Tasmanian tiger (an extinct Australian marsupial, not actually a cat) but in the game Crash Of The Titans he was redesigned and looks more cat like now.
Dingodile has a crocodile tail but the rest of him looks like some kind of pig thing, not a dingo.
The Buzzy Beetle enemies (which are basically fireproof Koopa Troopas) from the Super Mario Bros. series games actually look more like hunchbacked, gray turtles than actual beetles.
Diglett and Dugtrio from Pokémon, despite being both called moles, actually don't even look like moles at all! (for one thing, neither of them have visible bodies) Drilbur and Excadrill, however...
There's also Sandshrew and Sandslash who are said to be mice, but look more like armadillos or a pangolin.
Caterpie is listed as Worm, but it's a caterpillar (as it appears in Japanese).
Blastoise evolves from two turtles, but his description puts him as "shellfish" (possibly because the cannon in his shell look like the tubes found in mussels; the Japanese one is just "Shell"). The same English and Japanese names apply to Kabuto (horseshoe crab) and Kabutops (a mix between the sea scorpion and the trilobite).
An interesting variation and double-subversion come from Rattata and Raticate. Originally, they were listed as rats in the games, but have since been retconned into being mice.
Snubbull and Granbull look nothing like fairies; they're clearly based on bulldogs.
Raichu is said to be a mouse, but more strongly resembles a gerbil or possibly a jerboa.
Pikachu is said to be a mouse, it looks more like a rabbit with a zigzag tail.
Psyduck and Golduck are said to be ducks. Well, Psyduck kind of looks like a cartoony duck. Golduck, on the other hand, looks more like a platypus.
Growlithe is said to be a puppy, but it has tiger stripes. Justified, in that Growlithe and Arcanine are loosely based off of the Shisa in Japanese folklore.
Weepinbell and Victreebel are said to be flycatchers. But are clearly pitcher plants.
Slowbro is said to be a hermit crab, but it looks more like a strange cross between a hippopotamus and a salamander with a shell on its tail (the shell is the only part that fits the name - and is possibly why in the original it's "Tenant"). Dwebble and Crustle on the other hand...
Scyther is said to be a mantis, but resembles a scythe-armed lizardman with bug wings and a small thorax in place of a tail.
Cyndaquil is also said to be a mouse, but more strongly resembles an echidna.
Azumarill is said to be a rabbit, but it has a mouse-like tail that carried over from Marill.
Wooper and Quagsire are said to be fish, but are closer in appearance to axolotls or mudpuppies.
Likewise, Mudkip, Swampert, and Marshtomp are also said to be fish, but more closely resemble salamanders.
Vigoroth is said to be a monkey, but it strongly resembles a sloth on steroids rather than any known species of monkey.
Vigoroth's line, which are based on sloths, is a strange case, as its original form, Slakoth, does look like a sloth, but Vigoroth looks more like a mix of a sloth and some kind of monkey. Slaking looks like a giant sloth mixed with a gorilla.
Cradily is said to be a barnicle, but it looks more like a sea lily.
Bidoof is said to be a mouse, but it looks more like a gopher or a beaver. Oddly enough, its evolution, Bibabarel is said to be a beaver and actually looks like one.
Torterra is said to be a tortoise, but it looks more like an ankylosaur.
Kricketot and Kricketune are said to be crickets. Though, Kricketot looks more like some sort of beetle and Kricketune looks like a mantis with a mustache.
Subverted with Snivy, Servine, and Serperior. While they are said to be snakes, they do have limbs (Snivy and Servine have both arms and legs while Serperior just has arm-like frills). Justified, in that prehistoric snakes did have limbs.
Tranquil is said to be a pigeon, but looks more like a cross between a pheasant and a hawk.
Stunky and Skuntank are supposed to look like skunks, but they have cat heads instead. Also, Skuntank looks more like a honey badger than an actual skunk.
Shelmet is supposed to be a snail, but snails don't wear helmets. Or dress like ninjas.
Chespin is supposed to be a hedgehog, but he resembles a rabbit or an otter.
Tyranitar's name would suggest a Tyrannosaurus rex, however it more closely resembles Godzilla than anything else note Who is himself supposed to be based (partially) on a T.rex while hardly resembling one . Tyrantrum finally brought a proper T.rex into the fold.
Fire Leo from Viewtiful Joe, despite being a lion actually doesn't even look like a lion at all. Joe actually calls him a dog, but he hates being referred to as such.
From the same universe, we have Lammy, a guitar-playing redhead sheep (note how her name is a play-on-words of "lamb") who more resembles a deer or calf, or a human with antlers, pointy ears, and round nose. Name one person who already knew she was a sheep without being told.
Evil the Cat from Earthworm Jim looks more like a deformed rat than a cat; compare him with Bob the Goldfish's burly cat henchmen (henchcats?). Also Psycrow doesn't look all that much like a crow.
Trouble Bruin/Maruyama from Dynamite Headdy looks like a cat but is supposed to be a bear.
Diddy Kong from the Donkey Kong series is apparently a chimpanzee, despite his tail. Also, Chunky Kong is supposed to be a gorilla like Donkey, but unlike DK, he stands upright like a human.
The Chasmosaurus from the second Carnivores game more closely resembles a Triceratops.
James Pond is claimed to be a cod, albeit that's mainly to have a "Robocod" pun in the second game. James is bright orange throughout, while real cods have a white underbelly and a dark green or grey topside.
Sash Lilac of Freedom Planet is supposed to be a dragon, but in actuality looks more like a purple cat-thing.
If it weren't for the title, you'd have no idea that the little people in blue robes with wild green hair in Lemmings were, in fact, Lemmings. As a Seldom Seen Species you might even expect actual Lemmings, which are mouse-like animals, to look similar, or even not realize that Lemmings were a type of animal at all.