The pygmy raccoon Procyon pygmaeus and dwarf coati Nasua nelsoni, both endemic to Cozumel Island, Mexico, are two of the most endangered carnivores in the world, and their persistence requires active management. However, the taxonomic status of these populations remains unclear. Therefore we investigated mitochondrial DNA variation using the control region to examine the genetic uniqueness and evolutionary history of these taxa. Using strict phylogenetic criteria, species-level uniqueness of the Cozumel taxa was difficult to discern based solely on haplotype groupings and identification of unique alleles. However, population genetic approaches indicate significant population differentiation between Cozumel and mainland populations and we suggest that these taxa should be treated as distinct management units from their mainland conspecifics. Coalescent analysis indicated that the pygmy raccoon diverged from the mainland about 3050–200 111 years before present (ybp) and the Cozumel coati 1263–82 896 ybp; dates that can be further constrained by incorporating known-age subfossil specimens from Cozumel as well as the geological history of the island. Thus, although it is likely that the island taxa colonized Cozumel before the Mayan peoples populated the island, we are unable to definitively reject the hypothesis that colonization by these taxa was not human facilitated.