The groups of red-bellied lizards had a small distribution area in the Pontic zone. The several studies performed on these lizard groups are based on taxonomy and systematics. Although there were several taxonomic or systematic researches on some species of this group, the phylogeographical pattern and species disturbing boundaries of this group is still not clear. In the present study, we aimed to resolve the taxonomic and phylogenetic relationships of the red-bellied lizards in Turkey, based on two combined mitochondrial gene fragments and one protein-coding nuclear gene (rag1). Also, we evaluated ecological niches differentiations among red-bellied lizard groups. The mitochondrial DNA genes were found to be highly polymorphic in this group. One hundred and one variable nucleotide sites were detected on the combined gene sequences. According to phylogenetic trees based on the maximum likelihood (ML) and Bayesian inference (BI), the red-bellied lizards group have three species groups; Darevskia parvula, D. adjarica and unnamed Darevskia sp. (candidate species for Darevskia genus). This situation was supported by high bootstrap and posterior probability values in the trees of mitochondrial DNA gene fragments. However, no genetic variation was detected according to nuclear DNA (rag1) sequence. Because the species groups have no overlaps in terms of their ecological niches, ecological niche modelling (ENM) results revealed differences among the groups of D. parvula, D. adjarica, and unnamed Darevskia sp. Besides, we detected no geographical overlaps among three species groups, since there were geographical isolation zones among the species groups of red-bellied lizard.