The Davis Mountains cottontail, Sylvilagus robustus, is an endemic species of the Trans-Pecos area of Texas. Although S. robustus previously was believed to be extirpated from the Chisos Mountains, we confirmed existence of a population. We examined intrapopulation and interpopulation variation in S. robustus, as well as the genetic relationship to the eastern cottontail (S. floridanus) using partial sequences of the mitochondrial cytochrome b and control region genes. Six morphometric traits relating to overall size and six cranial characters considered diagnostic for the two subspecies were used to confirm identification of specimens. Our morphological analysis suggested that specimens from the Chisos and Davis Mountains were S. robustus; however, low levels of genetic divergence between S. robustus and S. floridanus appeared inconsistent with species-level recognition for S. robustus.