This is at least partly an historical question, and I am not even remotely a biologist of any sort, so apologies beforehand if it's a little obscure.
I often wonder how many distinctions were made in pre-Renaissance times, between species of animals.
For example, though I'm sure there have always been those with enough of an interest in nature to tell subtle differences, how were lemmings or voles, for example, told apart from rats or mice? Or did this recognition of speciation only come later, once more detailed (intrusive) forms of analysis became common?
I've looked up the etymologies for vole, lemming and hamster and all are dated post-Renaissance, so at least in these instances it may be safe to assume that people might simply not have noticed the differences before closer study took place. But I guess there are other animals where the same question applies (particularly smaller, harder-to-scrutinise animals where there are a large number of species similar at a glance).
EDIT: Vole means field (same root as wold), giving rise to the 19th c. term volemouse, meaning that originally, mouse and vole were indeed seen as one and the same -- proof of point.
P.S. Of course, this question need not apply solely to animal species.