The population genetic structure of the Persian sturgeon (Acipenser persicus) in the 2, 3, 4 fisheries regions and Sefidrud River was investigated based on the DNA sequencing method during 2010–2013 sturgeon stock assessment in the south Caspian Sea . DNA samples were extracted using ammonium acetate, the quantity of DNA was measured at 260 and 280 nm using spectrophotometry by Nanodrop (ND 1000 model), and the quality was checked by 1% agarose gel electrophoresis. Two sets of mitochondrial gene (D-loop and cytochrom b) after synthesis were used for polymerase chain reaction (PCR). A Neighbor-Joining (NJ) tree was constructed for all haplotypes according to Kimura 2-parameter model using Mega Version 4.0.1, number of haplotypes, haplotype diversity (Hd) and nucleotide diversity and their corresponding variances, genetic divergence overall and between paired populations (Fst) by 10,000 permutations and exact test, the gamma distribution shape parameter for the rate heterogeneity among sites and nucleotide sequence, the historical demographic pattern of A.persicus using neutrality tests and mismatch distribution analysis (D test of Tajima and Fs test of Fu), also the concordance of the observed with the expected distribution under the sudden population model using the Harpending, s raggedness index (Hri) were analysed. All calculations were conducted using ARLEQUIN version 3.11 and DnaSP 4.0. The aligned mtDNA sequences of D-loop and cytochrom b genes were consisted of 500 and 700 base pairs (bp) respectively. 13 and 4 haplotypes were defined, the average haplotype diversity were 0.961 and 0.419, average nucleotide diversity were 0.038 and 0.002, The gamma distribution shape parameter were 0.19 and 0.20 indicating moderate mutation rate heterogeneity among sites in A.persicus. The lowest value of Fst for D-loop gene was calculated between Sefidrud and four fisheries region (-0.002) and the Fst values observed for cytochrom b gene was 0.04 with Nm=5.37 and not statistically significant. The exact test of population differentiation (non-differentiation exact P values) showed significant differences between Sefidrud and other areas (P ≤0.05) for D-loop gene and for cytochrom b gene was nonsignificant (P ≥0.05). The mismatch analysis produced a unimodal distribution of pairwise differences for both genes which was consistent with the sudden population expansion model. Tajima’s D and Fu’s Fs statistics were significantly negative (D= -0.84 and - 0.99, P>0.01; Fs=-0.220 and -0.079, >0.01). ARLEQUIN calculated the value of t as 13.65 and the time since population expansion was estimated to be approximately 1501 years before present based on the mutation rates for the control region and this value for cytochrom b gene t= 0.98 which population expansion time was 7.84 years before present. The results of this study based on D-loop gene showed that population of A.persicus in the Sefidrud River is differ from other studied areas. Therefore fisheries managements of this unique and valuable stock for restocking and conservation of gene pools is strongly recommended
