Rarely observed in the wild, the existence of the Andean mountain cat (Oreailurus jacobita) has been established based on only 3 skulls and 14 museum skins. The Andean mountain cat’s evolutionary relationship to other felids based on morphological characters is largely contradictory, with evidence aligning it with South American small spotted cats (ocelot lineage) or alternatively with pantherine lineage felids. Here we describe the phylogenetic distinctiveness and placement of the Andean mountain cat using DNA extracted from pieces of nine independent pelt specimens, including one confiscated from a trapper in 1995. A phylogenetic analysis of DNA sequences from three rapidly evolving mitochondrial genes (16S rRNA, NADH-5, and ATP- 8) indicate that the Andean mountain cat is a distinct species belonging to the ocelot lineage. Our findings suggest that the Andean mountain cat diverged from a common ancestor with the ocelot (Leopardus pardalis) and margay (L. wiedii) and exhibits moderate levels of genetic variation.