EARLY ANIME = FAIL
Well, not really, but my point is that the most commonly referred to 'fish' are seen out of the window of the S.S. Anne and in the cerulean gym (if you've seen them elsewhere, then fair enough) which were both early episodes. Early episodes are not reliable for continuity.
What makes "early episodes...not reliable for continuity"? Just because they weren't expecting the anime to go on farther than Kanto doesn't make those episodes any less in continuity.
Besides the early episodes showing actual animals, and the vegetation seen in almost every episode, the 9th movie has coral. And yes, coral is an animal.
I can find real-world animals being shown up until at least the Madden's Peak episode. And of course, they've been referenced numerous times in Pokedex entries.
EDIT: There's also the background noise that features birds and insects that's in almost every episode. Though from my understanding, it's often not as prominent in the dubs.
But randomspot555, says some other user, I haven't seen an animal in Pokemon in 5 years. Answer that smarty pants!
Well, it's just because the focus of the show is on Pokemon. With 493 Pokemon out there, there's more than enough to have Pokes in the background instead of using a real-world animal. But real-world animals do exist in Pokemon. The movies, games, manga *, and anime, with every one except the games actually showing animals, and all at least reference them.
*I'm not a fan of the manga, but my understanding is that they aren't necessarily all in the same continuity. So that might not be true for all manga.)