Knowledge of how a species is divided into different genetic units, and the structure among these units, is fundamental to the protection of biodiversity. Procyonidae was one of the families in the Order Carnivora with more success in the colonization of South America. The most divergent species in this family is the kinkajou (Potos flavus). However, knowledge of the genetics and evolution of this species is scarce. We analyzed five mitochondrial genes within 129 individuals of P. flavus from seven Neotropical countries (Mexico, Guatemala, Honduras, Colombia, Ecuador, Peru, and Bolivia). We detected eight different populations or haplogroups, although only three had highly significant bootstrap values (southern Mexico and Central America; northern Peruvian, Ecuadorian, and Colombian Amazon; and north-central Andes and the southern Amazon in Peru). Some analyses showed that the ancestor of the southern Mexico–Central America haplogroup was the first to appear. The youngest haplogroups were those at the most southern area analyzed in Peru and Bolivia. A “borrowed molecular clock” estimated the initial diversification to have occurred around 9.6 million years ago (MYA). All the spatial genetic analyses detected a very strong spatial structure with significant genetic patches (average diameter around 400–500 km) and a clinal isolation by distance among them. The overall sample and all of the haplogroups we detected had elevated levels of genetic diversity, which strongly indicates their long existence. A Bayesian Skyline Plot detected, for the overall sample and for the three most significant haplogroups, a decrease in the number of females within the last 30,000–50,000 years, with a strong decrease in the last 10,000–20,000 years. Our data supported an alignment of some but not all haplogroups with putative morphological subspecies. We have not discounted the possibility of a cryptic kinkajou species.