Three subspecies of Mus musculus have been recognized in Iran so far: Mus musculus musculus, M.m.domesticus and M.m.castaneus that they show notable variability of centeromeric heterochromatin Region(CHR). Specimens were collected from 20 locality in Iran. First The study was performed by the centromeric heterochromatin banding (C-banding) and calculated their size in karyotype analysis software. Then Morphological differences in the CHR among 64 speciemens of the species Mus musculus from east and central of Iran were studied by the outline-based geometric morphometric method. Results indicated that all Specimens had 40 acrocentric chromosomes and all chromosomes had fixed position for the centromere. Results showed the same size of C-banding material in each locality but variation in the size of CHR on different localities. Specimens from northeast(NE) had smallest rang of CHR in their chromosomes and these areas had similar CHR in all of chromosomes in each locality. specimens of Zahedan and Zabol showed larger size of CHR in their karyotypes. Generally, chromosomes 4,5,6,7,8,9,10,11,12,14,15,16 and 19 showed high variability in their size of CHR and chromosomes 1,2,3,13,17,18 and X had low variability in size of CHR. Also chromosome 4 had large size of CHR in all populations and chromosomes 15,17 and 19 show smallest size of CHR in populations. Results of shape comparison , Centriod size analysis and cluster analysis in speciemens of east and central of Iran showed two groups and indicate a high morphometric distance among Speciemens of Zahedan and the other speciemens.

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