This study focuses on the strategy for the conservation of masu salmon, Oncorhynchus masou , in the northern part of the species range (via the masu populations in Sakhalin Oblast), based on data of its population structure. It is shown that masu populations that inhabit different rivers genetically differ from each other in allele frequencies at microsatellite markers. In the Naiba River basin, at least two genetically distinct masu populations exist: in the upper reaches and in a tributary, the Bolshoy Takoy River. The masu populations on Iturup Island significantly differ from those on Sakhalin Island; within Sakhalin, the masu salmon from the Chernaya River in the southwestern part of the island is genetically distinct from the southeastern Sakhalin and Aniva Bay populations. The genetic diversity of Iturup populations is substantially lower than that on Sakhalin, probably due to their small sizes. The measures for the conservation and recovery of masu salmon populations should be based primarily on their own genetic resources, or, in the case of a lack of spawners, on the base populations of their ecological/geographical region. In the latter case, masu populations of large rivers can be considered as base ones: for southeastern Sakhalin, this is masu salmon of the Naiba River; for Aniva Bay, this is masu salmon of the Lyutoga River. Transplantation of fish, fertilized eggs, or any other genetic material from a population that is different genetically and inhabits the waters with different ecological gradients should be strongly restricted. The formosan masu salmon from Taiwan Island is studied as an example of a strict genetic isolate.