Aggressive Retsuko has a very large number of obscure animals. These animals include red panda, (Retsuko and Lester/Resasuke) fennec fox (Zelda/Fenneko), spotted hyena (Heinrich/Haida), maned wolf (Wolfgang/Ōkami), Komodo dragon (Scatherine/Tsubone), secretary bird (Eaglette/Washimi), caracal (Carrie/Kara), Pallas's cat, capybara, axolotl (Yokosawa), spotted seal (Lucille/Gomakawa), prairie dog (Doug/Anai) and mandrill.
Chiyo's dog Tadakichi-san is a Great Pyrenees. They're not particularly rare in real life but rarely appear in fiction.
In one episode Sakaki ends up befriending an Iriomote cub she calls "Mayaa", a rare type of wild cat native to the Iriomote island of Japan.
Cage of Eden is filled with extinct animals that you would not normally see in popular culture. In fact, the series doesn't even feature the iconic Mesozoic reptiles such as non-avian dinosaurs.
In CLANNAD, Sanae Furukawa mentions that her greatest fear is the Bengal monitor lizard. Her husband Akio talks Tomoya into dropping a toy one down her back. Hilarity Ensues.
Cowboy Bebop has Ein the data dog, specifically a Pembroke Welsh Corgi.
Cute High Earth Defense Club LOVE! has a wombat, which for audiences outside Australia is a rare sight. For those in Australia, the hedgehog would be a rare sight. In both cases, Goura's shoebill is rare. However, note that these animals are aliens who look like animals and function as Mentor Mascots to the Magical Boy teams, zigzagging the trope.
Daikyouryu No Jidai featured Dunkleosteus, Eusthenopteron, Meganeura, Eryops, Placochelys, Tylosaurus, Ornitholestes, Clidastes, Corythosaurus, Edaphosaurus, Protoceratops, Scolosaurus, Henodus, Camptosaurus, Gorgosaurus, Acanthopholis, Deltatheridium, Pliohippus, Australopithecus, Homo habilis, Homo erectus, Moeritherium, and Tetralophodon.
Dinosaur Expedition Born Free featured Gorgosaurus, Polacanthus, Stegoceras (referred to as Troodon), Monoclonius, and Taniwhasaurus (referred to as the "Ezomikasa Dragon" and portrayed as a theropod dinosaurnote in reality it was a mosasaur).
While most of the dinosaurs in Dinosaur War Izenborg are commonly-seen genera, there was also Gorgosaurus, Tarbosaurus, Ceratosaurus, and Monoclonius.
Most of the Dino Knights in Dinozaurs are based on commonly-seen genera, but two of the three Dino Weapons take the form of Archelon and Kentrosaurus with the third being the relatively well-known Pachycephalosaurus. Also, the Cerazaur Brothers consist of a Centrosaurus and a Torosaurus (Chasmosaurus in original Japanese dub) along with the stock Styracosaurus.
"Nobita's Dinosaur 2006" prominently featured a Futabasaurus named Piisuke. Alamosaurus, Maiasaura, Baptornis, and Alphadon appear as well.
"Nobita and the Island of MiraclesAnimal Adventure" has rhinoceros beetles, Ceratogaulus, Chalicotherium, Elasmotherium, Gastornis, Glyptodon, moas, and Paraceratherium.
"New Nobita's Great Demon-Peko and the Exploration Party of Five" featured aardvarks as steeds for the humanoid dogs, a Congo peacock in the opening, red-crested turacos, a bushbaby, okapis, black-and-white colobus monkeys, a crowned crane, pangolins, bongo antelopes, African clawless otters, and great blue turacos. The rhinoceros that chases Gian in one scene looks more like a white rhino, as opposed to the more commonly used black rhino.
"Nobita and the Birth of Japan 2016" has steppe bison, crested ibises, Japanese giant salamander, Palaeoloxodon naumanni, and Machairodus.
The Jungle Book has Kichi the red panda, Tabaqui the striped hyena (in contrast to his original book species where he is a jackal), and Chil the Brahminy kite. The anime also features several Indian fauna such as sambar deer, langurs, mugger crocodiles, and dholes. Episode 10 showed Asiatic lions and a giant Komodo dragon.
Kemono Friends: One of the main characters is a serval. The single-episode animals featured are all over the place in terms of obscurity, ranging from very well-known (otter, lion), to nigh unheard-of (margay, campo flicker), and everywhere in-between.
Killing Bites has Brutes Civet and Pangolin, two unusual species used as bases for the animal-human hybrids.
Kimba the White Lion features many types of obscure African wildlife such as okapis, kudu, and dik-diks.
The anime movie adaptation of The Magic Tree House featured Alamosaurus, Brodavis, Borealosuchus, and Alphadon.
Hanako from Massugu ni Ikou is a Kishu, a Japanese breed of dog. When her boyfriend Mametarou learns this it only makes him feel worse about being a mix breed. Most of the other dogs are more frequently seen breeds like Shih Tzu's and Yorkie's.
Murenase! Shiiton Gakuen features all sorts of animals, both extant and extinct that aren't commonly seen in Manga, such Alamosaurus, aye-aye, naked mole rat, wallaroo, tarsier, Diprotodon, quagga, wooly spider monkey, Andrewsarchus, Baiji, Barbary lion, Steller's sea cow and more.
Fishmen and merpeople in One Piece are always based on and referred to by a species/type of fish or similar sea animal (i.e. a ray fishman). Some of them are quite rare in fictional works, like kissing gouramis, Japanese cat sharks, saw sharks, blue-ringed octopi and pike congers.
In Pikaia, this applies to basically all the extinct animals included, such as the titular pikaia and the anomalocaris. Even applies to some modern creatures like shipworms.
Pingu in the City: Besides the penguins based on emperor penguins from the parent series, there's also ones based on rockhopper penguins, adelie penguins, and gentoo penguins.
Ponyo on the Cliff by the Sea has rays, oarfish, coelacanths, bioluminescent squid, hagfish, flapjack octopi, anglers, sea slugs, Opabinia, Dipnorhynchus, Bothriolepis, Gogonasus, etc.
Four of the five main characters of Tokyo Mew Mew are actually infused with the DNA of an Iriomotecat,◊ an UltramarineLorikeet,◊ a FinlessPorpoise,◊ and a Golden LionTamarin◊ respectively. The idea is that, as these are all endangered species, their desire to continue living is what gives the girls their powers. The fifth is the somewhat more common wolf.note However, both species of wolf that were native to Japan are extinct. Also, a character introduced for the video game gets her powers from the DNA of a Humboldt Penguin.
The film has a Chilantaisaurus, Avisaurus, Ornithocheirus, and titanosaurs. The film also prominently features Maiasaura, which is while a stock dinosaur hardly depicted in the media. Tylosaurus and Giganotosaurus make brief appearances as well, and Troodon are featured in the opening attacking the Maiasaura nesting grounds.
The second film distributed by Korea has a Pawpawsaurus named Kirari, as well as Kronosaurus and Tapejara.