The distribution and relationships among populations of Caiman crocodilus crocodilus and Caiman yacare were investigated throughout Brazil. Caiman c. crocodilus inhabits the drainages of the Rio Solimões/Rio Amazonas, Araguaia, Araguari, Itapicuru, Paranaiba, Negro, Tapajos, Tocantins, Xingú, and the rivers draining to the Atlantic Ocean on the northern coast of Brazil. It does not occur in the Rio Saõ Francisco. Caiman yacare is endemic to the Rio Mamoré, Rio Guaporé, Rio Paraguai and Rio Paranã river systems and all of their lowland drainages. The northernmost limit for C. yacare lies between Costa Marques (12°25'S, 64°10'W) and Guajara Mirim, Pacaas Novos on the Rio Mamoré (10°55'S, 65°15'W). Small populations of apparently hybrid individuals were observed in the upper Rio Acré, the Rio Abunã, the upper Rio Madeira, and the Rio Mamoré between Guajara Mirim and Abunã. Caiman c. crocodilus and C. yacare populations are geologically separated and morphologically distinct. The taxonomic recognition of Caiman species with overlapping distributions in the states of Mato Grosso and Mato Grosso do Sul appears to be without merit.