Ellobius remains are common and often abundant in southeastern Europe, western and central Asia archaeological sites. A correct identification of species is crucial for our understanding of the evolution of species and communities through time, including biostratigraphic sequences to be established. This study applies geometric morphometric methods (GMM) to Ellobius first lower molars, with the objectives: 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 used in this paper includes specimens belonging to the three species that today occur in the southeastern Europe, western and central Asia: Ellobius fuscocapillus, E. lutescens and E. talpinus. The archaeological material comes from Late Pleistocene Iranian site of Kaldar Cave (Khorramabad valley, Lorestan Province, western Iran). Our study shows that the shape of the anterior cap and the arrangement of the following triangles allow discriminating 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.