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Kamchatka mykiss (Parasalmo O. mykiss) is an object of the Red Book of Russia, and its resident form (mikizha, rainbow trout) is one of the most valuable objects of world aquaculture and fish farming. At the same time, the status of this species is debatable; there is no consensus of opinion among authors regarding its genus. Different authors assign mikizha to the genera Salmo, Parasalmo, or Oncorhynchus. Some researchers believe, as before, that Kamchatka steelhead and freshwater are different species rather than two forms of the same species. Kamchatka mikizha has a complex intraspecific structure and rather strong phenotypic distinctions of individuals even within one water body. Only in Asia, most of wild populations of Pacific salmon have been preserved. Their habitats are in areas almost inaccessible, which makes them a unique object for the study of the problem of the group origin, microevolution, species structure, and speciation. In our work we tried to explore the different populations and locality of using two types of specially designed species-specific markers: SCAR and ISSR - markers. We created seven SCAR-and seven ISSR-markers which have significant population-variability of DNA-products from Kamchatka mikizha geographical group, which can be used in further studies of the species Parasalmo (O.) mykiss. The sequences of SCAR-markers were placed in a Gene-Bank, number EU 805500 - EU 805506. After research of samples from the west (river Sopochnaya, Utkholok, Tigil, Sedanka and Kol’) and the east coast (river Zhupanova, Bystraya, Elovka and Dvuhyurtochnaya) of Kamchatka, and out-group samples from Chile and North American , we obtained a new data are well supported by previously studies of this species. By SCAR-markers all populations of Kamchatka mykiss is strictly divided along geographical lines, with clearly observed the proximity of the North American and Chilean populations. In the other group are the Kamchatka populations, but the West Kamchatka group occupies a separate domain, and the East Kamchatka group tends to Chilean populations. This is especially pronounced in populations from the Zhupanova river. This similarity is very interesting and needs further investigation. Proximity is Chilean and North American groups are well explained by the fact that the mykiss inhabiting in the rivers of Chile has a North American origin. The value of ΘST (analog FST (Weir, 1995)) on average over all loci takes the values 28%, it is statistically significant value. By ISSR-markers were obtained similar results with the difference that the population of the East Kamchatka river Zhupanova clustered with North American populations. The value of ΘST for this type of research was even higher - 34%. These results were also confirmed in our laboratory studies of these samples at microsatellite loci. This work was supported by the Russian Foundation for Basic Research (grant no. 11-04-00778-a), by the grant of the Presidium of Russian Academy of Sciences for the leading scientific schools (grant no. NSh-2104.2008.4), Federal Agency of Science and Innovations within the framework of the Federal Target Program “Scientific and Scientific–Pedagogical Personnel of Innovative Russia” (state contracts 02.740.11.0461, 14.740.11.0633, 14.740.11.0165 15).