The genetic diversity of 56 samples of rainbow trout ( Oncorhynchus mykiss ) from 8 breeding centers located in Tehran (T), Chaharmahal and Bakhtiari (CB), Kohgiluyeh and Boyerahmad (KB) , Fars (F), West Azerbaijan (WA), Lorestan (L), Qazvin (Q) and Mazandaran (M) provinces in Iran, was examined using control region (D-loop) sequencing. A part of 700 bp of D-loop region was amplified using a pair of primers and 489 bp was sequenced successfully for 55 out of 56 samples. Brown trout ( Salmo trutta ) D-loop region was used as an out group for phylogenetic tree development. The highest and lowest nucleotide diversities were related to Adenin (32.01%) and Guanine (15.68%), respectively. From 489 bp sequenced, 22 polymorphic and 467 monomorphic sites plus 24 mutations and 19 haplotaypes were determined. Haplotype and nucleotide diversities were 0.844 and 0.00432, respectively. 14 out of 22 variable sites were only observed in one individual, while, 8 parsimony sites were repeated more than once. The highest haplotype diversities (1.00) were observed at samples belong to M and CB, while the lowest ones (0.524 and 0.667) were observed at WA and T, respectively. M (0.00873), F (0.00662) and CB (0.00526) show the highest nucleotide diversities, while the lowest nucleotide diversities were measured at WA (0.00156), T (0.00324) and Q (0.00351) populations. Haplotype network showed that three wide haplotypes were presented in most populations while the rest haplotype were repeated only once. In general, the nucleotide diversity within populations was low, however the highest and lowest average of nucleotide diversity were observed in the M(0.0088) and WA (0.0016) populations respectively. The majority and minority of nucleotide diversities were between M and Fand between WA and Trespectively. The highest divergence was observed between the population of M with F (3.429) and CB (0.345) and the lowest of that, observed among the population of WA with T (0.995) and Q (1.245). The results of AMOVA test showed that 99.04% of the variation was related to within populations. Based on F ST value, it could be concluded that genetic differentiation among population was very low. Finally, based on phylogenetic diagrams, it could be stated that the separation from the common ancestor was happened recently. The results of this study can be used in breeding programs for this economical importance species in Iran. Keywords : Haplotaype diversity, nucleotide diversity, phylogenetic diagram, haplotaype network, genetic differentiation.