Whether cranial measurements or pelage color is most appropriate for identifying two subspecies of gray squirrel (Sciurus c. carolinensis and S. c. fuliginosus) has been a matter of debate. The objective of this research was to examine populations of gray squirrels in Louisiana, Arkansas, and Mississippi to determine which aspects of variation are more useful for identifying subspecies. Cranial variation was assessed using 14 cranial measurements of museum specimens. Pelage color was assessed from digital pictures of the dorsal pelage. We used multivariate analysis of variance (MANOVA) to test for differences in cranial and pelage color variation. Cranial size was significantly different among populations of gray squirrels, with a north to south cline of larger to smaller individuals. However, we were not able to definitively assign populations in the zone of intergradation to a subspecies based on cranial morphology. Pelage color showed no discernable pattern of geographic variation among populations. Based on these results, we suggest that the differences observed among populations could be due to clinal variation and the legitimacy of S. carolinensis subspecies is tentative at best.