The Collared peccary (Pecari tajacu) is one of the three extant recognised species of the family Tayassuidae living in the Americas. To understand phylogenetic relationships among Collared peccaries, two mitochondrial and four nuclear DNA markers of specimens from six countries were analysed. Phylogenetic analyses of mitochondrial sequences showed that Collared peccaries clustered in two major clades, representing North-Central American and South American specimens. Collared peccaries from Colombia split between these major clades. Analyses of nuclear sequences showed a distribution of DNA variants which was consistent with mitochondrial sequence analyses. However, there was an uncoupling of nuclear and mitochondrial sequence variation in two specimens from Colombia. A comparison of pairwise genetic distances between mitochondrial sequences showed that the geographically widespread Collared peccary consists of two unique lineages as genetically distinct as the White-lipped and Chacoan peccaries as well as recognised species of the related Suidae family. This study has implications for breeding programs and efforts to conserve this species. It has also provided a phylogenetic framework to assess captive specimens of unknown origin in Australia and to assess claims to the ‘new’ Giant peccary species in the Amazonian forest in Brazil.