Rainbow trout ( Oncorhynchus mykiss ) is the best type of cultivating cold water fish in Iran. Different populations of this type is available in proliferation centers that cause reduction in production and increasing losses in this type of fish. The subject studied in this thesis needs caring aboat broodstock in order to maintaining genetic diversity, implementation of cultivating programs and choosing broodstock as native broodstock bank in populations. In this study, genetic diversity of this breed or sampling 204 pieces of broodstock fishes from 8 provinces was studied; It was studied in ChaharMahal Bakhtyari (CH), Kohgiloye Boyer ahmad (Y), Fars (F), Lorestan (L), Mazandaran (M), Tehran (T), Ghazvin (Q) and Azarbayejan – Gharbi (AGH) by means of PCR – RFLP method. DNA was extracted by using Aluminum Acetate from Caudal fin. PCR reaction was done by using a pair of primer nucleotide production in ND5/6 part of mtDNA moleculs. In order to enzyme digestion for PCR product, 10 endonuclease were used. Enzyme digest patterns were observed using 6 polyacrilamid gel and silver staining. 5 enzymes ( Hinf I , Taq I , Rsa I , Bshf I , Ava II) showed polymorphism. The results showed 32 composite haplotypes. Among these samples, in Y fish farm the number os 13 haplotype as the maximum haplotype number and after that in L fish farm 9 haplotype number was found. The average of Rainbow trout cultivating haplotupe diversity and nucleotide gene in defferent zones respectively was 0.8152 ± 0.032 , 0.007736 ± 0.00434. The most haplotype and nucleotide diversity was registered in L and then Y fish farms. The least haplotype and nucleotide diversity respectively was found in M and CH farms. The most nucleotide difference was among L and M farms by 0.02234 and the least difference was between T and F farms by 0.00215. Also it was illustrated that the most portion of Heterogenous Rainbow troutis among farms belonging to AGH, L and Y farms. Based on Fst, most of the difference observed between populations is 0.7684 was obtained between AGH and Q and opulations and the least differences was obtained 0.0286 between T and CH. According to tree diagram graphs, AGH and Y was placed in separate branch.. Due to the results, we can claim that AGH, Y and L farms samples areindependent populations of Rainbow trout and also can be considered in cultivating programs. Keywords: Oncorhynchus mykiss , PCR-RFLP، ND5/6, Genetic diversity, Haplotype compositions, nucleotide diversity
