We investigated the genetic structure of Metapenaeus affinis population from the northern coasts (Khuzestan Province:Bahrakan and Lifeh-Boosiaf region) of the Persian Gulf, using five microsatellite markers. The samples of pleopods tissue ofshrimp were taken, DNA extracted and PCR was performed on microsatellite primers. The results revealed that all fivemicrosatellite loci were polymorphic, the number of alleles (Na) ranged from 5 to 12 per locus, and the observed and effectivenumber was 7 and 3.67, respectively, also the observed and expected heterozygosis was ranged from 0.1 to 0.77 and 0.1 and0.83, respectively, which indicated that the two populations of M. affinis possessed a rich genetic diversity. The deviationfrom Hardy–Weinberg equilibrium (P
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