Quite a few groups. The Aztecs had some presence in the region; as did the closely related Nawat (Pipil) people (though they were more focused in El Salvador). Numerous Mayan groups, including the K'iche', Itza, and Mam, for example. Some unrelated populations, like the Xinka. Even today, the country's got a population that's roughly 40% indigenous, much more if you count the mestizo majority.