Loss of genetic diversity decreases the population or species will or may affect the ability of a population being in a new environment affect or cause disease. Estimation of genetic diversity in fish farms will playan essential role in managing it properly. Therefore, this study aimed to estimate the genetic variation between the three population of rainbow trout including Iranian, French, and Danish using mitochondrial DNA COX1 and Cytb genes were performed. Ninety samples from three populations salmon farms in the area of Kalat Naderi city of Mashhad collected. DNA was extracted and COX1 and Cytb gene were amplified by PCR and then sequenced. The results showed a low level of genetic variation within studied populations. Phylogenic and haplotype analysis revealed that the genetic distance between Iranian trout population and French was much lower than Danish. This finding might indicate that the Iranian population might have the similar gene pool with and originated from the French population.

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