In Russia, only low amylose short grain varieties were previously grown, but recently, because of the growth of consumption of this cereal, domestic varieties with various quality have become necessary. Absence of information on the genetics of this trait constrains selection in the given direction. Despite a considerable number of foreign works on localisation of genes defining quality of rice grain, there are no similar Russian works yet. Definition of the possibility of using loci identified from studying foreign samples, for marker assisted selection of domestic germplasm became the purpose of our research and possible localisation before the unknown loci defining the quality of rice grain. We used both neutral markers and those associated with quality. Polymorphism of the allocated groups of varieties with the contrasting quality trait was studied using 57 markers. Polymorphism of domestic varieties of rice with contrasting quality traits such as “weight of 1000 grains”, “translucency”, “husk content”, “the maintenance of the whole kernel in a croup” was studied with use of the SSR markers to reveal chromosomal regions associated with the division of Russian rice varieties into groups based on the traits being studied. It was shown that 12 markers authentically divided groups with the various grain form, 3, with a various exit of the whole kernel, and 1 marker group, with various translucency and husk content. The markers authentically dividing groups of varieties with various weight of 1000 grains, groats exit, the protein and amylose content were not revealed. Data about the association of markers RM3276, RM5707, RM5508, RM7110, RM509, RM600, RM136 with the quality trait in references were not revealed. Probably, the genes defining the quality of rice grain, specific for domestic gemplasm, are located around the given markers.