PCR amplification and direct sequencing of regions of the cytochrome b mitochondrial genes was carried out on Iranian populations of the salmo trutta fario species.  Samples of salmo trutta fario were also examined and used as an out group in the phylogenetic analysis. Results based on 1192 bp indicated differentiation between fario morphs from Iran and other salmonids also Iran and other country had collected. Despite the large phenotypic differences within salmonids, very low genetic variation was found. On the basis of the cytochrome b sequences studied, Salmo carpio and Salmo fibreni, which have been described as good species, there were high homology between salmo trutta fario , salmo trutta and salmo trutta caspius (99%), but regards salmo salar the rate of homology 93%.  Regards salmo trutta fario, in hatchery trout has not red colour strips time of hatchery in salmo trutta fario whereas has a bluish grey body colour, However, they are larger than Atlantic salmon, salmo trutta caspius and salmo trutta, more regular in shape, and less intensively pigmented, moreover there are red spots are always observed in populations, however, the shape and size of salmo trutta fario is different with salmo trutta caspius and salmo trutta but the among of homology were high (99%). The salmo trutta fario and salmo trutta caspius are living in the Rivers of North of Iran that connected to Caspian Sea; perhaps these species with themselves has been conjugated, and regards salmo salar is living in the Atlantic Ocean and other Sea and Rivers connected to it, that so far to salmo trutta fario populations in Iran. However we cannot report exactly that how much homology between sequences, because already there are not complete sequence in GeneBank regards salmo trutta caspius and salmo trutta fario.