See instinctively that's what I would have figured (and it surely was the intention when making Gen 1), but the fact that they never fixed it to make them the same species in the pokedex and a few other details made it feel like I could play it that way. For example, assuming Nidoran are the same species it's the only pokemon whose sexual dimorphism not only leads to different evolved forms, but means that its base form has different stats. They have a slightly different moveset, too, which is also unique.
Is calling them different species a bit of a stretch ? Absolutely, by all means Game Freak just never bothered fixing that early stuff, just like they never bothered fixing Mr. Mime to adjust for the creation of gender. But it was more fun that way, and was vaguely justifiable, so I just went with it.