Conodonts from ninety samples of the Bashkirian Monte Alegre, the Bashkirian–Moscovian Itaituba, and the Moscovian–lower Permian Nova Olinda formations were recovered from twenty-three wells and one quarry in the Amazonas Basin, Brazil. Palaeontological systematic study focuses on Adetognathus, Diplognathodus, Idiognathodus, Idiognathoides, Neognathodus, and Streptognathodus species. Several taxa are evidenced for the first time in the Bashkirian to Moscovian of South America, and one new species, Idiognathodus itaitubensis, is proposed. Conodonts confirm the known affinity of Amazonian faunas with those in the Midcontinent-Andean Province. The occurrence of Idiognathodus izvaricus suggests the possibility of an occasional connection of the Amazonas Basin with the western Palaeo-Tethys Ocean during the Moscovian. Finally, a few specimens of Streptognathodus occur in Upper Pennsylvanian to Permian beds of the Nova Olinda Formation.