Archeological evidence indicates that a dwarf fox (Urocyon sp.) has inhabited Cozumel Island, Mexico at least since the arrival of Mayan peoples, but no taxonomic descriptions or morphological assessments of the animal exist. A recent field study indicates that this fox is on the verge of extinction and therefore it is critical to describe the population. Because no skins or complete skulls of the Cozumel fox exist in museum collections, we examined subfossils collected during archeological excavations of the human-waste middens of Mayans who inhabited the island c. 1500–500 years before present. Measurements of 37 bones from a minimum of 12 adult individuals suggest that this animal is diminutive (the body size was c. 60–80% of mainland specimens), similar to other Carnivora from Cozumel that are recognized as distinct species. Estimated rates of character differentiation for mainland and island foxes under a range of possible divergence periods (1000–130 000 years) suggest that the Cozumel fox population has been isolated for a minimum of 5000–13 000 years, and perhaps far longer. Colonization of the island by Urocyon therefore likely predates the colonization of Cozumel by humans.