Pacific noble salmons of the genus Parasalmo (Oncorhynchus) have a latitudinal amphipacific distri bution and exhibit a high level of variations in the behavioral, morphological, and ecological features, which determine the wide range of life strategies and intraspecific forms. The species Parasalmo (Oncorhyn chus) mykiss (rainbow trout, mykiss) is one of the most interesting members of this genus showing a high adaptability, morphological plasticity, and an extremely wide distribution. In the Asian part of the range, the mykiss is of particular scientific and practi cal interest, since here this species is represented pri marily by the wild type populations that have retained their original population structure. This makes salmon a unique object for studying the problems of the origin, formation of the wild type population structure, mechanisms of microevolution, and speciation pro cesses. An important feature of the Kamchatka group of mykiss populations is the depletion of the genome in the Asian part of the range [1] and a small number of effective population genetic markers. The phyloge netic subdivision of the Kamchatka mykiss popula tions was studied insufficiently and primarily by our group of authors. In the previous studies, the geo graphical differentiation was determined using alloz ymes [2], SCAR markers developed in our laboratory [3], and microsatellite locus analysis [4]. The aim of the present study was to develop new techniques and increase the number of such population significant genetic mark ers by analyzing poorly studied DNA regions.The high variability, which can be used in the pop ulation analysis, is characteristic of the inter satellite DNA loci (ISSR PCR, inter microsatellite PCR). This method has been widely used in the practice of multilocus mapping of the genome since 1994 [5]. This method has a high resolution and is used in phy logenetics mainly at the level of populations and closely related species [6]. However, this method has not been used earlier to study the population genetic relationships of the Kamchatka mykiss. Earlier, we have created seven original ISSR markers specifically for this fish species [7]. In the present study, we evalu ated the efficiency of using these markers for genetic differentiation of myukiss populations in Kamchatka.The study was performed on the same material ( Table 1) that was used in the previous study per formed with SCAR markers [3].The DNA isolation method, the tests for determi nation of DNA quantity and quality, the selection of ISSR primers, and PCR conditions were described in detail in our methodical work on the development of ISSR markers [7]. The reproducibility of results in dif ferent experiments was tested three times using seven pairs of primers. When amplification reagents manu factured by the same company were used, the results were reproduced in 100% of cases.The frequency of null alleles was calculated by the formula proposed by L.A. Zhivotovsky for diploid objects studied using multilocus dominant DNA markers [8]. The allelic d...