Peromyscus sonoriensis is a widespread species ranging from southern Texas to the Yukon, from the Mississippi to the Pacific. Because of this extensive range, there are substantial differences in morphology due to variation in temperature, precipitation, and habitat. We used 2 data sets (n = 4,840 and n = 20,175) to study morphological differences of their crania and appendages. Consistent with Allen’s rule (shorter appendages with colder temperature), both data sets show a strong, positive, correlation between tail length and the average January temperature. However, there was an equally strong, but negative, correlation between tail length and average July temperature. We observed similar results for feet and crania. Ear length had a significant negative correlation with July average temperature but no correlation with January average temperature. When we controlled for temperature, cranial and appendage length increased with latitude, which was opposite of what we expected. Furthermore, longitude had a strong impact as mice trapped further west had longer appendages. When divided into habitats, forest deer mice are more likely than prairie or desert deer mice to demonstrate morphological responses to differences in climate, location, and year trapped. Our results show that P. sonoriensis exhibit notable morphological variation linked to location, habitat, and climate.