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In everyday life you're unlikely to know anyone of a different species to yourself, besides pets. And however much you might love your furry/scaly/feathered friends, the relationship probably isn't quite the same as the bipedal ones you have.
In fiction, this restriction is way more lax, especially in the realms of of Fantasy and Science Ficton. Those worlds are populated by a whole host of fantastic aliens, elves, werewolves, robots, vampires, and who knows what else. Its incredibly common for people of completely different species to become close friends. Since the majority of these creatures tend to have an intelligent on par- if not greater- than that of humans, it might actually be stranger if people of various species didn't develop some sort of kinship. Even for species that are Always Chaotic Evil, you can expect at least one individual to throw off his hat and say My Species Doth Protest Too Much, joining the good guys.
Sometimes, in universes where the existence of other magical/advanced races are part of The Masquerade, or there's a lot of Fantastic Racism going on, these friendships might be more limited. This will usually allow people to comment how strange the hero(e)s' friendship is.
Anime & Manga
- Ash Ketchum and series mascot, Pikachu, from Pokémon. Friendship, trust, and understanding between trainers and their Pokémon are recurring themes on the show.
- Jesse and James with Meowth. This is different than any of the other examples from this show because Meowth is treated more like a equal than a Mon or pet. This is probably because he is one of the few Pokémon that speak human.
- Rem (Shinigami) and Misa (human) of Death Note. Rem develops a platonic love for Misa and is even willing to die for her. Light (human) and Ryuk (Shinigami) also fall under this having a few Villains Out Shopping moments together, though they are of a more vitriolic type.
- Hellsing has Integra and Pip (humans) with Alucard and Ceres (vampires).
- Wolf's Rain had a pack of wolves and a genetically engineered flower-human hybrid.
- Kimba and Roger Ranger from Kimba the White Lion.
- Used in Black Jack, with a human scientist who's a friend of Black Jack adopting his last experiment (a super-intelligent deer) and treating him like a brother. It Got Worse soon.
- Also between a young fisherman and a whale. Again, It Got Worse when the whale was blamed for the death of some fishermen. Unlike the scientist and the deer, they get better.
- Mickey Mouse and Goofy.
- Pictured above: In the X-Men there is Kitty Pryde and Lockheed the Dragon, who is her friend, not her pet.
- Human Rick Jones and the Kree Captain Marvel (Mar-Vell as well as Genis-Vell).
- She-Hulk and Jazinda the Skrull.
- Most of Superman's friendships qualify, though not necessarily Clark Kent's.
- The Wolfrider elves and their wolves in Elf Quest, partly because they can exchange feelings telepathically, and partly because they're related by blood.
- Nextwave has a human, two superhumans, a mutant, and a robot.
- From the Grimms' collection:
Films -- Animated
- This is common in Disney and Pixar films:
- Mickey Mouse, Donald Duck and Goofy (dog?) going back to before World War 2.
- Genie (a genie) and Aladdin (human) in Aladdin.
- In The Lion King, Zazu (bird) and Mufasa (lion). Also Timon (meerkat) and Pumbaa (warthog), close friends who later befriend Simba. (lion)
- The Fox and the Hound. Between, well, a fox and a hound.
- Lilo and Stitch, a human and a genetically engineered alien monster.
- Finding Nemo comes to mind, where not only do different kinds of fish get along, but they also befriend sea turtles, and even species that otherwise prey on fish, such as sharks and pelicans.
- The Jungle Book has Mowgli the human (who was literally raised by wolves) befriending Baloo the bear. They also friends with Bagheera the Black
- Oliver and Company has Oliver the cat befriend Fagin's dogs.
- The Rescuers, along with its sequel, involves mice talking to and befriending humans. The first even has a cat talking to and befriending both humans AND mice. The sequel also has Cody feeling very attached to Marahoute the eagle, though they can't communicate with each other.
- Bolt has a trio of three different species: Bolt (a dog), Mittens (a cat) and Rhino (a hamster).
- Toy Story: While Andy does not know his toys are alive, they do care a lot about him. Woody in particular gos to great lengths to return to him when separated. Said toys are also True Companions with each other.
- The title character of Tarzan is friends with a gorilla and an elephant.
- A Bugs Life has several different insects and arthropods as friends.
- In Mulan Mushu the dragon is friends with Mulan (human), Crikee (cricket) and Khan (horse). Villain Shan Yu has his falcon.
- In The Land Before Time, a long-neck ("Brontosaurus"), three-horn (Triceratops), swimmer (Saurolophus), flier (Pteranodon) and spike-tail (Stegosaurus) overcome their parents' generations-long racism and become True Companions. A sequel adds a sharp-tooth (Tyrannosaurus Rex) to the gang and the TV series adds a Oviraptor.
- Ice Age: Manny and Diego and Sid form one of this type of friendship with each other by the end of the first film and it continues into the second film and third film.
- Shrek, (an ogre) Donkey and eventually Puss in Boots become friends in the Shrek films.
- The wolf-dog Balto is friends with a Russian goose and two polar bears.
- The title character of Spirit (a horse) appears to be friends with an unnamed bald eagle and he later befriends a human.
- San (human) and her wolf brothers from Princess Mononoke. And then there's her "mother", Morro.
Films -- Live-Action
- Blade (Dhampyr) and Whistler (human)
- Dragonheart features the friendship of a man and a dragon.
- Star Wars has Han Solo and Chewbacca, the Wookie, as friends and partners.
- The Jungle Book, The Second Jungle Book, and the Just So Stories by Rudyard Kipling are full of friendships between humans and animals - Mowgli, the adopted wolf and friend of Baloo the bear, Bagheera the panther, and Kaa the python is only one example of many - and between different species of animals.
- Winnie the Pooh: Features a human boy and his friends, who are
toysa bear, pig, tiger, rabbit, donkey, owl, and two kangaroos. The animated series adds a gopher.
- The Twilight books and films, which feature friendships and romance between humans and vampires, werewolves (technically shape shifters) and humans, and friendships between werewolves and vampires.
- In the book Fire World, Rosa (A human) and Alleron (A Firebird) are friends.
- In The Lord of the Rings, the Fellowship consists of representatives of five species and races (Elves, Humans, Dwarves and Hobbits, plus Gandalf the Maia). Hobbits Pippin and Merry also later become friends with the Ent Fangorn, while Gandalf numbers Gwaihir the Wind-Lord (an intelligent eagle) among his friends.
- A number of examples from the Discworld novels, notably in the Ankh-Morpork Night Watch, starting with Detritus the Troll, Cuddy the Dwarf, and Angua the Werewolf in Men at Arms.
- Good Omens has Aziraphale (an angel) and Crowley (a demon).
- The Book of Night with Moon has Arhu (a cat) and Ith (a t-rex).
- Dragonriders of Pern in which humans form lifelong bonds with intelligent dragons.
- Animorphs has Ax, an Andalite, and the five human characters. Or four human characters and one red-tailed-hawk/human/Andalite (Tobias). The team also count Hork-Bajir and Chee among their friends and allies. Cassie even befriended a Yeerk.
- The core premise of Dinotopia is human/saurian friendship.
- If You Give a Mouse a Cookie has a friendship between the eponymous mouse and the nameless protagonist.
- Harry Potter is friends with Dobby, a house-elf, which is considered odd because most wizards treat them as inferior slaves. Before him, Regulus Black had a similar relationship with his house-elf Kreacher.
- Harry, Hermione, Ron and a fairly large number of the Hogwarts staff are also friends with Hagrid, a half-giant. The slightly strained relationship with Hagrid's full giant brother might fit this trope better, though.
- The Horse and His Boy, about the friendship between...well...
- Dean (a human) and Castiel (An angel) in Supernatural.
- In Doctor Who, all of the Doctor's companions aside from his granddaughter Susan, as well as Romana, fall under this.
- Star Trek is stuffed to the brim with this.
- As is Babylon 5. A particularly odd one is between Londo (Centauri) and G'kar (Narn), who are the ambassadors of two warring species--one of which (the Centauri) had previously conquered and enslaved the other--and started out hating each other. Circumstances force them to tolerate and eventually like each other, if a bit snarkily.
- Buffy the Vampire Slayer and the spin-off Angel had several frienships between humans, vampires, werewolves, and demons.
- Lexx had a human, a half-human lizard girl, an undead assassin, a robot head, and a living spaceship.
- Farscape had a human, Human Aliens, and Starfish Aliens.
- Stargate SG-1 - the Stargate team (humans) with Teal'c (a Jaffa).
- Tracker Mel and Cole-Although Mel is a Half-Human Hybrid, that only came out in the next to last ep of the series, so it was viewed as human and alien for most of it.
- The Planet of the Apes series had two humans (Virdon and Burke) and an ape (Galen).
- Roswell, with its human and alien teens.
- Twilight Princess casts Link (a Hylian) and Ilia (human) as childhood friends... and maybe more. But don't tell that to Zelink or MidLink shippers. Link later befriends the imp-like Midna, a Twili.
- Early in Suikoden II, the player is given the opportunity to recruit Kinnison and his dog companion (who's actually a wolf), named Shiro.
- Yuri Lowell and Repede from Tales of Vesperia. Bonus points since Repede earns two titles specifically regarding his friendship with Yuri:
- "Sinful Sidekick", which is earned after he witnesses Ragoh's death at Yuri's hands.
- "Considerate Sidekick", earned after he leads Karol and the others to Yuri, for trying to strike off on his own.
- Sonic the Hedgehog and Miles "Tails" Prower also count: one's a blue hedgehog (that can run at mach speeds), the other's a twin tailed fox... who can fly.
- Mass Effect, where Commander Shepard can develop close, non-romantic friendships with several different kinds of aliens.
- In Dragon Age, no matter your race, you can befriend elves, dwarves, humans, and Qunari.
- In Metroid Prime 3, Samus can count among her friends Rundas, a Phyrigisian and Gandrayda, whose species is unknown, though Gandrayda seems to love piling on the Les Yay.
- In the Paper Mario series, your friends include Goombas, Koopas, Lakitus, Boos, among others.
- Okami has Amaterasu, a sun goddess in Big Badass Wolf form, and Issun, a Poncle.
- Super Mario Bros. has humans, dinosaurs, and mushrooms living in the SAME KINGDOM. For a specific example, Mario and Yoshi are best friends.
- Disgaea Hour of Darkness Flonne with Laharl and Etna.
- Pokémon Mystery Dungeon has you and your partner. Yes, it has been mentioned that Pokemon are all the same species, but it still counts.
- An important Aesop in all of the Pokémon games, but especially Pokémon Gold and Silver and the remakes, is that Pokemon should be friends and partners to their trainers, instead of just tools.
- In Blaz Blue, we have the trio of Noel Vermillion, Tsubaki Yayoi (two humans) and Makoto Nanaya (squirrel girl). This has such a great effect that the formerly prejudiced-for-her-race Makoto is incredibly loyal to those two and makes it her mission to ensure no harms come between them, and anyone who does get horribly killed by her hands (Or so she says for the latter), and the mere thought of her friendship to them is the one thing that enables her to survive the Boundary like Hakumen, and be immune to Terumi's infamous Trolling.
- Pretty much every Furry Comic ever.
- Florence (Uplifted Animal Big Badass Wolf) and Sam (Alien Sqid) in Freefall.
- The Inexplicable Adventures of Bob: Bob is friends with dragons, unicorns, bigfeet, aliens, robots, mutants, giants, and furry lab accidents.
- Chatoyant College: Corrie/Dawn and Professor Lal, the gang and Troy, and Dawn and Tom
- Avatar: The Last Airbender also has this with Aang and his sky bison, Appa. Later, he befriends Momo (his pet Lemu) as well; which isn't surprising since Aang's a Friend to All Living Things.
- George of the Jungle comes to mind.
- In Futurama there is Bender and Fry, and to a lesser extent the other members of the Planet Express crew. Also Zoidberg.
- In My Little Pony Friendship Is Magic the unicorn Twilight Sparkle is friends with her assistant Spike, a baby dragon. And Fluttershy is friendly with most non-pony animals and beasts. There was also Pony/Buffalo friendships, Pony/Zebra friendships, and until recently, a Pony/Gryphon friendship.
- Adventures from the Book of Virtues has two human kids, a bison, a red-tailed hawk, a bobcat, and a prairie dog.
- Voltron: Legendary Defender has the Paladins (all human save for the half-Galra Keith, but he does pass as a human) and Coran (Altean), especially regarding Lance. Doubles as Intergenerational Friendship since they're in the 15-25 age range and he's the Altean equivalent of a middle-aged man.
- Allura (also Altean) with all the Paladins, save for Lance - since they can potentially go into Interspecies Romance.
- Towards the end, there's potential for this between the humans of the Galazy Garrison and the half-Galra Acxa. Curtis and especially Veronica are at least willing to try it.
- They say a man's best friend is his dog. Cats, birds and horses are also common companions.
- Koko the gorilla used to have a pet kitten.
- This news story tells of Gohan and Aochan - a dwarf hamster and rat snake, respectively - who peacefully share an enclosure at a zoo in Japan (or shared, most likely, due to the average lifespan of hamsters and the article being written in 2006). Gohan was intended to be Aochan's lunch when the snake refused to eat frozen rodents, but Aochan never showed any hostility, eventually taking to frozen food. They got along so well that Gohan could safely climb onto the snake's back to take naps.