Cruciferous plants (Brassicaceae family) are affected by different kinds of phytopatogenes, and one of most harmful is bacteria Xanthomonas campestris pv. campestris Pam. (Dow.), which is affects crucifers to bring on black rot. Strains of X.campestris are dividing into physiological races, which one can reveal by reaction of varieties with race specific genes of virulence, but existence of 9 races of pathogen complicates the interpretation of published results of plant resistance evaluation. One of the traditional methods to investigate the genetic basis of variation within the germplasm of a species is genetic mapping based on segregating populations or quantitative trait loci (QTL) mapping. QTL mapping is based on the principle that chromosome loci or genes and markers, which are saturated linkage groups of mapping population, segregate via chromosome recombination during meiosis, thus allowing their analysis in the progeny and detecting linkage disequilibrium between phenotype and the genotype of markers. To achieve our goal we have used this approach in present work too. For clarification of peculiarity of heredity of race specific resistance two mapping populations of DH lines of Brassica rapa (DH30: P115 x Р143, obtained by crossing turnip and yellow sarson, and DH38: Р175 x P143, obtained by crossingpak-choi and yellow sarson) were evaluated for resistance to strains of four X.campestris (Xcc) races and two races X. arboricola (Xcr).Upon evaluation to resistance of DH lines of two B. rapa mapping populations to strains of bacteria Xanthomonas (В-32, 1279а, 5212-I, PWI231, Я-3004, Ов-3028), it was revealed monogenic non-linked heredity of resistance trait for 4 races of Xcc, and at the same time resistance for Xcr strains has been determined by two dominant genes. Carried out QTL analysis allowed obtained for population DH30 five markers linked to resistance for five races of pathogen in linkage groups R03, R07, and R09. For population DH38 it was obtained 16 SSR makers linked to resistance for six races of pathogen substantially in linkage groups R01, R02, R03, R04, R06, R08, and R09, and one marker was found in linkage groups R05 and R10. For example, for DH 30 molecular marker KS50200, localized in R03, was linked with genetic locus of resistance to three Xanthomonas races (1279а, В-32, Ов-3028), and marker SSR89, localized in the bottom of R07 – with loci of resistance to two races (5212-I, B-32). Levelof variabilityexplained by revealed QTL was from 2.7%till 28.3%. Gene effects at all revealed loci were additive. In R05 and R10 it was found one marker for each linkage group respectively. At upper part of R01 revealed marker BRMS096R01, linked with resistance of DH38 to four races of pathogen (1279а, 5212-I, B-32, Я-3004). At the middle of R03 localized marker BRMS043 of the resistance locus to three races (1279а, B-32, Ов-3028), and at the bottom part of the same linkage group – marker Na12E02 of the locus resistance to two races (1279а, B-32). At the bottom of R02 revealed marker Na12H09N12 of the locus resistance to two races (5212-I, PWI-231), in upper part of R04 – Na10D09R04 which marked locus resistance also to two races (B-32, Я-3004), at the bottom of R06 – markerВС51 of the locus resistance to three races (1279а, Я-3004, PWI-231), and in the middle of R08 – marker Ra2E12R08 of the locus resistance to two races (B-32, Ов-3028). In the upper part of linkage group R10 it was found CAPS marker of FLC1 locus resistance to race 5212-I, which is also linked with many important traits of plants such as ascorbic acid and carotene content. Than by the use of selected molecular markers it was carried out SSR analysis of mapping population lines contrasting for resistance to different pathogenraces. As a result of molecular and genetic analysis it was found molecular markers of loci of resistance for all Xanthomonas races used at present investigation. The work is supported by grant of RFBR 10-04-00446-a.