Morphometric analyses were carried out on Testudo graeca from west-central Morocco, and compared to previously published mitochondrial DNA sequence variation. We measured 41 characters on 244 tortoises from three localities, including one population of T. g. soussensis from Souss Valley. All three populations could be statistically differentiated in a multivariate space using these characters. The population from the Jbilet mountains was the most differentiated (no overlap), those from Essaouira on the coast and from Admine showed limited overlap (5%). Sexual size dimorphism (males < females) remained constant between sites. Sexual shape dimorphism was prominent in all populations, but the degree of dimorphism differed for some characters when corrected for size. Tortoises from Jbilet living under harsher conditions (low precipitation, high thermal amplitude, low plant cover) were smaller, lighter, more flattened and less dimorphic in shape than the others. Although the Admine population (currently assigned to T. g. soussensis) was morphologically distinct, its distinctiveness was less supported than in the case of Jbilet; several other qualitative traits previously considered as defining this subspecies were also questionable. Moreover, this morphological variation contrasted with the available genetic evidence (12S rRNA mtDNA) which did not reveal significant variation between any of the populations. This implies that morphological differences have either arisen very recently or can be attributed to phenotypic plasticity. This should be taken into account when using morphological traits for taxonomic considerations and conservation management.