Considering the importance of genetic studies to manifest inter population differences in species, samples of Artemia partenogenetica were collected from seven inland lakes including Shoor and Inche-Borun lakes in Golestan Province, Hoze-Soltan and Namak lakes in Qom Province, Maharloo and Bakhteghan lakes in Fars Province and Mighan pool in Markazi Province. A total of 210 samples were subjected to DNA extraction by phenol-chloroform method. Primers were designed on a ribosomal fragment (16SrRNA) of the species' mtDNA sequence and the PCR was conducted on the samples. Digestion of the PCR product with approximately 1584bp lengths by 10 restriction endonuclease (AluI, EcoRI, Eco47I, HaeIII, HindIII, HinfI, MboI, MspI, RsaI, TaqI) showed 12 different haplotypes: 4 haplotypes in Shoor and Inche-Borun, 1 in Namak and Hoze-Soltan, 3 in Mighan pool, 1 in Bakhtegan and Maharloo and 3 in Maharloo. Haplotype diversity values within collected samples varied from zero in Hoze-Soltan, Namak and Bakhteghan samples to 0.7425 in Inche-Borun and Shoor while nucleotide diversity varied from zero in Hoze-Soltan, Namak and Bakhteghan, to 0.0077 in Mighan. The minimum nucleotide diversity among samples was zero between Hoze-Soltan vs. Namak and the maximum was 0.1700 between Inche-Borun and Shoor vs. Mighan. Nucleotide divergences among samples were least in Inche-Borun vs. Shoor (%-0.02) and most in Inche-Borun and Shoor vs. Mighan (%16.18), averaging to %3.40. The evolutionary distances between 12 haplotype showed that the maximum value belonged to Mighan haplotypes vs. Inche-Borun and Shoor haplotypes. Regarding the digestive patterns produced by each enzyme in the studied region, Eco47I is introduced as the population-specific marker of A. partenogenetica in Iran. Test of population differentiation based on haplotype frequencies were statistically significant (P≤0.001) with the exception of Hoze-Soltan vs. Namak and Inche-Borun vs. Shoor. We conclude that there are enough evidences in haplotypic level for dividing A. partenogenetica in Iran into five populations: Hoze-Soltan and Namak, Mighan, Maharloo, Bakhtegan, Incheh-Borun and Shoor.