Genetic variation of stellate sturgeon, Acipenser stellatus, from the North (Volga river) and South (Gorgan river) Caspian Sea was investigated using NADH 5/6 gene and PCR-RFLP analysis. In this study, a total of 60 samples of stellate sturgeon from the North and 14 samples from the Southern Caspian sea were collected. MtDNA ND 5/6 gene was amplified by polymerase chain reaction (PCR). PCR-product digested using 31 end nucleases restriction enzyme. Five of the 31 enzymes showed polymorphism (RsaI, HinfI, HpaII, HaeII/, MboI). Totally 18 composite heliotypes among 74 samples were detected. Haplotypes AAAAA, BAAAA, ABABA from the Vo]ga river showed 28.33%, 11.66% frequency, respectively, and from the Gorgan river heliotypes AAAAA, BAAAA showed 64.28% and 14.28% frequency, respectively.Average haplotype and nucleotide diversity within the populations in Volga river was 0.88±0.027 and 0.0122 and in Gorgan river was 0.5934±0.144 and 0.00398, respectively. Average nucleotide diversity and nucleotide divergence among populations of North and South Caspian Sea was 0.008644 and 0.000542, respectively.Monte-Carlo simulation using 1000 replication showed no significant difference between sampling site in the southern and northern Caspian Sea (X2=0.926±0.0083).