The Mosul bleak Alburnus mossulensis Heckel, 1843, in Iran is widely distributed in Fars, Isfahan, Tigris and Bushehr basins. Considering the importance of the genetic variation and population structure for management and conservation of species, especially native fish, the genetic diversity of Mosul bleak was investigated using molecular techniques. In this study 30 specimens of Mosul bleak were collected from each locality (Konjancham, Kashgan, Gamasiab, Doroud and Dopolan rivers) and 25 specimens from Davoud Arrab River. For molecular study, DNA was extracted using ammonium acetate method and Takara kit from bodies tissues collected from each stations. The DNA quality was examined by electrophoresis on 1% agaros gel and painted with ethidium bromide. PCR amplification was performed using four pairs of microsatellite primers (CypG24, BL1-2b, BL1-98 and Rser10) at annealing temperature 56 ° C. PCR products electrophoresed on 12% achrylamid gel and painted with silver nitrate. Calculations were done using PowerMarker ver 3.0, PopGene ver 3.2, ARLEQUIN ver 3.11, MEGA ver 4 and NTSYS ver 2.02 software. Number of the observed alleles at all loci ranged from 8 (BL1-98) to 14 (CypG24) and averaged 10.75 alleles per locus. Allele sizes at CypG24, BL1-2b, BL1-98 and Rser10 loci were in the range of 138-215, 141-180, 272-300, 176-240 respectively. The mean of polymorphism information content (PIC) at all loci was 0.835. Among the pair four markers, BL1-98 was the lowest polymorphic and CypG24 was the highest polymorphic one. The expected heterozygosity ranged from 0.79 in Davoud Arrab River and 0.84 in Konjancham and Kashgan rivers and averaged 0.825. The observed heterozygosity ranged from 0.69 in Konjancham River and 0.81in Kashgan River and averaged 0.75. Significant deviations from Hardy–Weinberg Equilibrium expectation were found at BL1-98, BL1-2b and CypG24 in all population and Rser10 in Davoud Arrab population ( p 0001). The analysis of molecular variance (AMOVA) indicated that the percent of variance among populations, Among individuals within populations and within individuals were 2.01, 15.6 and 82.4 respectively. Only a small proportion (2.01%) of the variation was attributed to differences between the populations and large proportion of the variation was attributed to differences within individuals. The overall value of F ST values between populations and basins were 0.02 and 0.0071 respectively. The genetic similarity and distance index came in the range of 0.696-0.894 and 0.111-0.34, respectively. The level of genetic variability was high in the studied populations but comparison of mean expected heterozygosity values revealed that these loci did not show significant differences between the populations. Although no significant genetic variation between the populations of bleak, existed significant genetic differentiation was found between them ( p 005). The low genetic structure could be due to high gene flow. For better understanding of population structure of Mosul bleak, population structure studies using other molecular techniques from all distributed areas followed by ecological and/or biological researches should be considered. Keywords : Mosul bleak ; Alburnus mossulensis ; microsatellite; population variety; genetic differentiation