Juniper Publishers- Journal of cell Science Abstract In order to investigate the mitochondrial haplogroups in a selective population of Isfahan province, 96 unrelated men in Isfahan province with at least two generations in this province were token blood. Then DNA was extracted and quality assessed. 25 coding SNPs defining the major haplo groups that occur in Africa, Western Eurasia and Eastern Eurasia were selected and combined into two multiplex genotyping assays. Each one consisting of a PCR step and a SNaPShot step. Then for support of our detective haplo groups by SNaPShot system, D-Loop region was sequenced in some samples. : In this province Western Eurasian haplo groups were predominant. Haplo group U and H (22%, 21%) and then T, J and U8b (11%, 10% and 7%) had the most frequency. Eastern Eurasian haplo groups (C, D, R9, R11, M and N) were present at a lower frequency and a North African haplo group (M1) at frequency of 1%. Keywords: mtDNA; SNP; Haplo gr