In this study we provide data on morphological and morphometric variation in specimens of Peromyscus zarhynchus from 6 different geographically isolated localities in Chiapas, Mexico. We found significant differences in the mean greatest skull length in all specimens examined of P. zarhynchus, but we did not find differences in other cranial and external variables related to age, sex, and individual variation. The individuals examined from different populations of P. zarhynchus showed distinctive morphometric characters correlated with their distribution, and probably to feeding changes related to different types of vegetation and weather in Chiapas.