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In Lost Eden an important character and narrator is a pterodactyl. There are other dinosaurs.
https://www.gog.com/game/lost_eden
So many great new candidates, here are the additions to the list:

Ys VIII: Lacrimosa of DANA
Tomb Raider 1+2+3
Inspector Waffles (Coming soon)
Lost Eden
Orwell's Animal Farm
Backbone (Coming soon)

Nicohvc persuaded me regarding Ys 8 and also the first Tomb Raider games all in all are filled with animals.
Creaks has relevant NPCs that are bird people
Ethan: Meteor Hunter "is supposed to be a rat"
http://www.seaven-studio.com/indies-going-all-in-with-self-publishing-an-ethan-meteor-hunter-post-mortem/
Omensight is made by the same devs of Stories and like Stories is set in a world inhabitated with animals.
Tanglewood®
New Super Lucky's Tale
Kao the Kangaroo Trilogy
Post edited February 15, 2021 by nicohvc
Okay, time to update the list, there have been some interesting releases lately:

Creaks
Ethan: Meteor Hunter
Omensight
New Super Lucky's Tale
Kao the Kangaroo Trilogy

I would also add:
Spiritfarer, in which many animal spirits appear
Jet Kave Adventure, in which are present a lot of prehistoric animals
Nine Noir Lives (Coming soon), with once again a cat detective

I had excluded Tanglewood because it would seem to be effectively an alien creature on an alien planet.
Armello - anthro animals.
Master of Magic - includes various anthro animal races/units, and animal units.
Post edited February 19, 2021 by Garran
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Garran: Armello - anthro animals.
Armello is not sold here anymore...It was a couple of years ago but it got delisted.
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alexandros050: Armello is not sold here anymore...It was a couple of years ago but it got delisted.
Mentioning a delisted game, it's not focused on animals but in Death Gate, Legend point and click, there is a cool section with a dog. The dog enters your party and follows you around for a small part of the game. But alas, it's not on GOG for now.
Post edited February 26, 2021 by Dogmaus
To be fair, it might be the case of including delisted games with a note, as some users at least of course still have them.
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Garran: Armello - anthro animals.
Master of Magic - includes various anthro animal races/units, and animal units.
Thank you, added:
Armello (Delisted)
Master of Magic

I feel the same way as Dogmaus, with a small note we can add the removed games as well.
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Alexim: Thank you, added:
Armello (Delisted)
Master of Magic

I feel the same way as Dogmaus, with a small note we can add the removed games as well.
If so, the dog in Death Gate is a companion for a good part of the game and also playable.
Not focus on animals, but in Dark Seal (Gate of Doom) you can be turned in a harmless pig for short amounts of time. Very cute and funny.
https://ibb.co/VNHssJz
Also, there is a spell that turns the player in a giant rat/mouse that uses smaller ones as an attack.
Plenty of dragons, and a Chinese dragon as well.
Post edited March 04, 2021 by Dogmaus
No one mentioned The I of the Dragon yet?