Ellobius remains are common and often abundant in southeastern Europe, western and central Asian archaeological and paleontological sites. A correct identification of species is crucial for our understanding of the evolution of species and communities through time. This study analyses molar size and conformation on Ellobius first lower molars (m1), through the two-dimensional Geometric Morphometric Methods (GMM), using TPSdig2 and R softwares. Fourteen landmarks were placed at the maximum curvature on the salient and re-entrant lingual and buccal angles, on the posterior lobe and the anterior cap. In order to characterize the size and shape of the anterior cap, 60 equidistant semi-landmarks were automatically positioned along the curve corresponding to the external outline of the tooth enamel from the buccal salient angle 3 to the lingual salient angle 4. Our work: 1) to discriminate modern species and explore morphological and size differences in reference samples; and 2) to identify fossil specimens recovered in archaeological sites, based on the aforementioned analysis. The reference dataset includes specimens from the three species occurring today in the southeastern Europe, western and central Asia: Ellobius fuscocapillus, E. lutescens and E. talpinus. The fossil material comes from Late Pleistocene Iranian site of Kaldar Cave. Our study shows that the shape of the anterior cap and the arrangement of the following triangles allow to discrimine the three studied extant Ellobius species. The shapes of E. fuscocapillus and E. lutescens m1 appear rather similar, whereas Ellobius talpinus is well separated from these two species. The total length and the anterior cap of m1 in E. fuscocapillus is greater than in Ellobius lutescens. The GMM analyses performed on the modern reference dataset allowed us to identify fossil specimens from Kaldar Cave as E. lutescens and some as E. fuscocapillus, and excluding E. talpinus.