Rice is an important grain crop known for its ability to grow in flooded soil. Sometimes rice plants resist weeds and herbicides’ application ineffectively and unprofitably. The varieties that have flood-resistant genes can help solve this problem, so the study of DNA markers is of great importance. Flood-resistant loci contain the Sub1 gene, which is activated under anaerobic conditions. The locus contains three similar genes Sub1A, Sub1B, Sub1C, but only the gene Sub1A improves resistance to such conditions. The purpose of the study is to find the most effective Sub1A marker for identifying genes for tolerance to prolonged flooding in domestic hybrid rice samples as a natural method of weed control. As donors there have been used foreign varieties (Inbara-3, BR-11, TDK-1, IR-64, CR-1009, Swarna), and Russian varieties (Novator, Magnat, Stepnyak, Bakhus, Komandor, Kuban-3, Boyarin, Kontakt) as recipient forms. From the populations of F5-F9 generations, there have been selected 96 early maturing hybrids. To identify the gene in hybrid plants, three sets of locus-specific primers, the most widely used according to the literature, were used: Sub1A(1F1R), Sub1A(2F2R), and Sub1A(3F3R).The region amplicon Sub1A(1F1R) was found in 17 samples among 96 studied hybrids, the region amplicon Sub1A(2F2R) was found in 17 samples, and the Sub1A(3F3R) primer has initiated nonspecific amplification and did not allow the identification of genotypes. To further verify the phenotypic expression of the introduced locus, the morpho-physiological response of all hybrid rice lines under flooding conditions was analyzed. Under flooding conditions, the number of germinated rice seeds in the parental lines (Novator, Boyarin and Stepnyak) decreased, as well as in hybrids that did not inherit the locus according to molecular genetic analysis. As a result, it is recommended to carry out analysis using two markers to improve efficiency.