By and large, pokémon and animals get along reasonably well. I say “reasonably” because of course wild creatures may display hostility to one another, and it’s true that pokémon wield powers no animal can defend themselves against. Furthermore, unlike humans, pokémon gain no benefit from coexisting with animals, generally speaking, so one would assume that the two don’t cohabit.
Yet strangely … they do. Pokémon actually treat animals with caution for the most part, and while animals are a bit rarer than pokémon, pokémon ensure that there is some sort of niche left for animal wildlife. Sometimes, the two even work together, to build nests, to hunt, or generally to survive. For example, sometimes, wild poochyena will hunt alongside wild coyote to take down larger prey. On the other hand, wild pikachu will often defend rabbits from hawks or snakes, and sunkern will sometimes help squirrels find new sources of nuts. (Then again, with the latter example, that’s partly because squirrels will otherwise eat sunkern.) Even outside of woodland environments, you have corsola serving as homes for fish, rattata leading urban rats to food caches, and so on and so forth.
In the home, meanwhile, most pet pokémon will get along quite well with pet animals. It’s just that pokémon will often perceive themselves to be a step between their human owners and their animal companions. That is to say, pokémon will often view themselves as caretakers for cats, dogs, and so forth, even though they realize they’re only pets for humans themselves.
That relationship has offered a lot of insight into the pokémon kingdom’s relationship to both mankind and the rest of the animal kingdom, actually. By observing the way pet pokémon interact with animal pokémon, scientists were able to form the current going theory: that pokémon view themselves as custodians of nature, in a way. That is to say, because they’re more in-tune with nature than humans are, they take on a role in which they accommodate and work hand-in-hand with the other creatures sharing their world. For humans, that means battling alongside them and getting stronger. For animals, that means living in harmony with them.
Unless, of course, the animals happen to be prey or vice versa. Squirrels eat sunkern, pidgeotto eat worms, and so on and so forth.