Bassaricyon (Carnivora, Procyonidae) is a little-known group of small Neotropical carnivores from central and northern South America. Despite their charismatic nature, they are difficult to spot in the field, and they are confused with another procyonid, the kinkajou. This poorly studied genus comprises four species: B. gabbii, B. alleni, B. medius, and B. neblina, the latter with two subspecies. In this study, the genetic diversity of Bassaricyon from eastern Amazonia was explored based on the mitochondrial gene cytochrome b. A maximum-likelihood analysis confirms the taxa recognized at the species and subspecies levels and shows that populations from the Guiana Shield (GS) are well structured relative to the lineage from western Amazonia (WA), with genetic distances among them comparable to those of other Bassaricyon subspecies. A median-joining network showed five median vectors between B. alleni lineages, more than between B. medius and B. neblina subspecies (n = 1); additionally, there are at least 10 nucleotide substitutions between them, suggesting a considerable difference between these lineages. In the last review of the genus, the estimated divergence time between B. alleni from western Amazonia and Guiana Shield was slightly less than that between B. neblina and B. medius subspecies, suggesting less time to differentiate. We collected Potos flavus in the two municipalities sampled; however, in different localities, suggesting different habitat specificities. These results, together with morphological differences among B. alleni lineages, suggest a subspecies taxonomic status for the Guiana Shield population, B. alleni beddardi.