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The Mexican kit fox (Vulpes macrotis zinseri) is an endangered subspecies that is restricted to the arid plains of the Sierra Madre Mountains of Mexico. Previous genetic analysis of other arid-land fox populations in the U.S. showed that the species is divided into two phylogenetically distinct taxa; the kit fox occupies the western, and the swift fox, the eastern plains bordering the Rocky Mountains. We analyzed 740 base pairs (bp) of cytochrome b sequence and 350 bp of control region sequence to determine if Mexican kit foxes are genetically distinct and to assess their relationship to kit and swift foxes of the U.S. We found two genotypes in 19 foxes from Nuevo Leon and Coahuila, Mexico that differed by a single base pair substitution. These genotypes were phylogenetically grouped with those sequences from kit foxes in Arizona, Utah, and New Mexico but differed from them by 1 to 4 substitutions (0.3 to 1.3%) in control region sequence. Our results suggest that the Mexican kit foxes are closely associated with populations of the kit fox to the west of the Rocky Mountains and, although they have unique genotypes, Mexican kit foxes have only recently been isolated from their conspecifics in the U.S.