In Tim Burton's Planet of the Apes, apes and humans are decended from those aboard the Oberon.
Where did the horses come from?
To be frank there is no explanation in the film itself. Looks like a plot-hole to me.
Or we can assume that the planet they land on always had horses. Same question is asked on many other sites too with no results.
Like from IMDb
Where did all the horses come from?
This is a tricky question to answer. It seems unlikely that horses would be brought on the Oberon for experimentation. It is up to viewers to come up with their own explanation.
So if I have to make guess I will say that planet was always inhabited with other animals like horses.
This is also got discussed over reddit and this is what a user came up with his speculation:
The easiest "consistent" explanation for horses is to assume that the animal facility just had horses too (in a different part of the station that wasn't on film). For whatever reason. I mean, there isn't really a good explanation to have every primate species on space station anyway.
Maybe we can pretend they were doing terraforming somewhere (they have gravity control, so they should be to pull it off). Horses were being exposed to "space conditions" to see what modifications were necessary to allow them to live on a new world, and so many primates were around to give the best possible sample of near-human studies in order to make sure there was no danger at all.
Which is not that convincing to me.
They were on earth the entire time. Horses were one of the few animals that didn't die off due to a disease. This is the same plot point from the original series, where time travelers introduced the virus that killed off pets and animals, leaving just mostly just Apes and horses.