Calomyscus is one of the most interesting genus of rodents presented in Iranian plateau. This group can be regarded as an example for integrative researches. It is distributed in rocky habitats in foothills and mountains region of Iranian plateau as isolated populations. Although karyological analysis is providing important information for their evaluation as different species, the taxonomy of genus Calomyscus remains somehow controversial and demands a revision on taxonomic value of new found isolated populations of this genus in Iran. Up to now 5 species have been reported in Iran, C. bailwardi from south and west, C. hotsoni from south east ; C. elburzensis from north east; C. grandis from north and C.urartensis in Azerbaijan region. For this study 76 specimens were collected from 11 localities and taxonomic determination performed by molecular methods including PCR- RFLP and sequencing of mitochondrial gene. The multivariate and landmark analysis of mandibles was done to obtain the taxonomic characteristics of each species. The molecular study confirms two major clade: 1- C. hotsoni and C.bailwardi, in South –west and 2- C.elburzensis and C.grandis in central and North-east Iran. C. elburzensis is composed of different isolated populati ons , one of which as new records was recently found in Yazd, center of Iran and Halali of Bejestan protected reserve in East of Iran belong to this species. So this species should be regarded as a complex species. This study also confirm that south-east of Iranian plateau should be the center of origin of actual mouse- like hamsters of Iranian plateau , that is in accordance with paleontological data reported by other authors . Finally the landmark analysis of mandible total shape space showed significant morphological differences and proved taxonomic character states that is beneficial for determination of each studies species of genus Calomyscus in applied studies like archaeozoology, paleontology and neotology .

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