The skull morphology of four species of cottontails from the mountains and plateaus of southwestern United States and northern Mexico, currently recognized as Sylvilagus nuttallii, S. cognatus, S. robustus, and S. holzneri (=S. floridanus holzneri), was analyzed using multivariate statistics. Based on 26 or 30 measurements taken on each of 350 adult skulls, and formulation of 16 pooled samples, with each representing a different geographic population, the results show there are two species-level distinctions in skull type. Cottontails from southern Utah, northern and east-central Arizona, and northern New Mexico show morphological overlap among geographically adjacent samples and all have a highly arched skull. These are referable to S. nuttallii. Cottontails from central Arizona, central New Mexico, and western Texas southward along the Sierra Madre Occidental to Durango, Mexico, and Sierra Madre Oriental to central Coahuila, Mexico show morphological overlap among geographically adjacent samples and all have a relatively flat skull. These are referable to S. holzneri. Both S. nuttallii and S. holzneri are polytypic in the study area. Sylvilagus n. pinetis is restricted to the White Mountains of Arizona. Those north and west of the Colorado River in Arizona and Utah are referable to S. n. nuttallii and those from southeastern Utah, northeastern Arizona and northern New Mexico are referable to S. n. grangeri. The population of cottontails previously referred to S. cognatus from central New Mexico is indistinguishable from topotypical S. holzneri from southeastern Arizona as well as populations from southwestern New Mexico, Chihuahua, and Sonora, Mexico. Cottontails previously referred to S. robustus, from the Guadalupe Mountains of New Mexico and Texas, southward in the mountains of western Texas, and the Sierra Madre Oriental to central Coahuila, Mexico, average larger in overall size and, on average, have proportionately larger auditory bullae and are referable to S. holzneri robustus. The relationship of S. holzneri to other mountain/plateau-inhabiting taxa, outside the study area in central and southern Mexico remains to be resolved.