Masu salmon Oncorhynchus masou has been listed as national second-class protected species in China, and many of its local populations have been under threats of decline because of environmental deterioration by human activity, such as habitat loss, water pollution, or dams. Genetic characteristics should be clarified in wild masu salmon population for an effective protection and recovery. In the present study, we explained genetic relationship and structure of masu salmon population in Mijaing River by sequencing the COI gene and analyzing microsatellite makers. Results of COI sequences analysis revealed 15 gene variable sites in approximately 696 bp, which defined 12 haplotypes, including some haplotypes related to geographic regions. The NJ tree indicated genetic relationship that we preliminarily inferred, that is, the masu salmon from Mijiang River belonged to the cherry salmon family (O. masoumasou). Results based on 14 microsatellite loci showed high haplotype diversity and low nucleotide diversity, indicating low genetic diversity of wild masu population in Mijaing River. The observed genetic structure was influenced primarily by bottlenecks due to overfishing and habitat loss. Since masu salmon has become highly vulnerable in China, we recommend to strengthen the protection of resident masu salmon population.