Genus Acomys comprising 14 species from mouse like rodents and substituted in Murinae subfamily. The aim of this research was surveying external, cranial and dental character differences among diverse populations of Acomys dimidiatus in Minab, Boushehr and Geno biosphere reserve. Sampling was performed during summer 2003 and 2005. Total of 52 species were collected from mentioned sites. The results of ANOVA revealed a significant differences of all characters between study areas except Length of Diastema and Length of anterior Palatine foramina. Analysis of PCA showed Khaeez and Jam samples (Boushehr region) was stand in separated group and had a positive relationship with second axis. These samples were similar by Cranial Width. Minab samples had an optimistic association with Occipitonasal Length, Condylobasal Length, Zygomatic Length and Length of Mandible. Some of Geno samples were similar to Minab samples but others were disparted because of negative relationship with Occipitonasal Length, Condylobasal Length, Zygomatic Length and LM characters. Comparisons of cranial characteristics revealed importance of Occipitonasal Length and Condylobasal Length to distinct populations. Our results suggested mentioned morphometric characters as a good index to separate individuals from different areas.