A total of 16 Sciurus anomalus and 10 S. vulgaris samples were collected from distributional areas in Turkey. Standard and geometric morphometric approaches were used to assess morphological characteristics of S. anomalus and S. vulgaris. Karyology was also studied for both species. Two mtDNA genes Cytb (959bp) and dLoop (482) were sequenced from both species to find the extend of genetic variation and the phylogenetic relationships. Standard morphological measurements were statistically tested for 26 cranial measurements and showed significant differences between the two species (P<0.05). A total of 13 landmarks from mandibles and 15 landmarks from the ventral side of the skull were utilized to analyze the shape variation. Based on the mandibles, the two species showed significant differences (P=0.013), but the ventral side of the skull did not (P=0.069). Karyological analyses indicated the same chromosome number (2n=40) but there were differences in the NF (S. vulgaris 76 and S. anomalus 80) and NFa (S. vulgaris 72 and S. anomalus 76) values. Both mtDNA gene regions separated two species into two different groups. Cytb sequences combined with the sequences obtained from Genbank and the sequences from both species were clustered with appropriate Genbank anomalus and vulgaris sequences. Two S. vulgaris populations in Turkey partially separated from each other. All northeast samples and the Thracian samples were separated, while the Edirne samples (from Thrace) clustered with the northeast squirrel population. The genetic distance between the two species based on dLoop sequences was d=0.182±0.020.