The Caspian Sea and its basin is one of the natural habitats of wild common carp Cyprinus carpio . Considering the importance of the genetic variation and population structure studies for management and conservation of species, the genetic diversity of wild common carp in the Anzali wetland was investigated, using PCR-RFLP technique. In this study 200 sexually mature individuals of wild common carp, were collected from five stations including, Siah Keshim protected area, Selke wild refuge, Sorkhankol wild refuge, Abkenar region and Anzali wetland estuary (40 individuals from each station). DNA was extracted using ammonium acetate method from fin clips. PCR amplification of the mtDNA D-loop region was performed using a pair of primer and produced a fragment with 420bp length. According to identifying this segment, two specimens from Abkenar and Sea sequenced and submited in Gene Bank by accession number GU225730 and GU320667 respectively. PCR product was digested using forty Endonuclease enzymes. Enzyme digested pattern were observed using 6% polyacrilamid gel and silver staining. Four enzymes; Tas I, Sma I, I, Apo I showed polymorphism. The results showed seven composite haplotypes among five stations. Haplotypes AABA and ABAB were recognized specifically in Abkenar station and haplotypes BAAA and BAAB in Siah keshim and haplotypes A and AAAB only observed in Sorkhankol station. Genetic distances between haplotypes ranged from 0.01334 to 0.35000. Average haplotype and nucleotide diversity were 0.1321 and 0.014196, respectively. Nucleotide divergence among population was measured as 0.0216. statistical Data analysis was performed using ? 2 test with 1000 interactions for detecting geographic heterogeneity. This analysis showed significant differences between different haplotypes among populations except between Abkenar and Siah keshim stations ( p ?0.5). Also, the ? 2 value for Selke and the Caspian Sea estuary, because of their similar haplotypes, was zero. This result showed that there is no difference between Selke and the Anzali wetland estuary stations. It can be concluded that the PCR-RFLP method in mtDNA D-loop region is a suitable marker for population studies of the wild common carp in Anzali wetland and Caspian Sea estuary and this species in the region consists of at least three populations, Abkenar-Siahkeshim, Sorkhankol, and Selke-Sea. Key Word: Wild common carp, Cyprinus carpio , PCR-RFLP, D-loop, Anzali wetland.
