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>Ponyta
Ponyta is a curious case. Originally, this line was only encountered in Pokémon Mansion on Cinnabar Island, Kanto. However Ponyta are described as frolicking in the fields and mountainous areas, and likely only appeared on Cinnabar Island due to their Fire typing. While they have been re-evaluated to roam Kanto's mainland since Yellow, they do not appear to have a consistent habitat, or exist in areas matching the PokéDex’s descriptions.
They’re also noted as being able to jump over tall Australian and Parisian landmarks, although the line ironically does not exist in Kalos and we are yet to see a region based on Australia.
Sinnoh has the Ponyta line roaming free in fields at the base of Mt. Coronet, exactly as they are described in the PokéDex. However, we can see that just south of the fields is the Solaceon Town ranch, and it is likely that these Ponyta were transported and bred in Sinnoh for the farmland.
This brings us to Johto, in which Ponyta, and more notably Rapidash, roam freely at the base of Mount Silver. It is very likely that the Johto travelers who traveled to Sinnoh and co-created the Sinjoh Ruins, took these Rapidash to travel through the mountainous, cold climate, explaining why Ponyta exist near the Solaceon farmland in Sinnoh.
With the exception of some appearances in the Sevii Islands, and the migration to the Unovan Route 12 fields, Rapidash is not found in the wild* protecting its young elsewhere in the Pokémon world, and as such I determine that the base of Mt. Silver is this Pokémons original natural habitat.
*Let’s Go does show Rapidash roaming the old Cycling Road. However it is unlikely this is the Pokémon’s natural habitat. Why would any Pokémon be native to a man-made bridge, contrary to the habitats described in the Dex, such as Mt. Silver?