In this study phylogenetic relationship of the Jajrud River Brown trout Salmo trutta L. 1758 in the Namak Lake basin was analyzed using complete D-Loop sequence of the mitochondrial genome, compared to other Iranian populations of the species. The results clarified that Jajrud brown trout, similar to other Iranian brown trout populations belongs to the Danube phylogenetic lineage. The observed haplotype in the Jajrud population is similar to the reported haplotype in the Karaj River. Based on the results the Namak Lake basin brown trout affined to the Caspian populations and its relationship to Salmo macrostigma was not confirmed.  Since the Karaj and Jajrud River haplotypes have not been observed in the Caspian Sea basin and because of its relationship to other Iranian and Danube haplotypes it is plausible to consider this haplotype as an old haplotype that also may exist in the Caspian Sea basin. According to the biology of Brown trout, geographic characteristics, and based on the properties of the Namak haplotype it may be inferred that the Namak Basin Brown trout populations are native to the basin and are not introduced.