In this article Gossypium mustelinum Miers ex Watt. interactions of the species with the species Gossypium barbedense L. and the inheritance of morphobiological and valuable economic traits (in particular, resistance to salt stress) in their hybrid generations were studied. Based on cross-breeding of G.mustelinum with G.barbadense and G.darwinii, the parameters of empty and full seeds were determined. The level of genetic polymorphism among the study samples was investigated using SSR markers associated with fiber quality traits and resistance to fungal diseases, salt and drought stress in a set of cotton microsatellites. The set of selected microsatellites was located along all chromosomes, where the most markers (20) were located on chromosome A06, and the least marker (1) was located on chromosome D13. Among the markers, HAU2768, NAU7049, NAU1151, NAU0868, CGR575, CGR6357, JESPR1304, Gh056, BNL3932, DPL0530 showed the highest polymorphism. Also, information content (PIC) and heterozygosity (He) values of polymorphic markers were studied. According to him, the lowest PIC value of microsatellites was 0.204 and the highest indicator was 0.375. Expected heterozygosity (H) – from 0.231 to 0.5, marker index – MI from 0.0128 to 0.576, discrimination power (D) – from 0.257 to 0.943, resolving power (R) – from 0.8 to 4.4 was found to be in the range. Also, their phylogenetic relationships were studied based on the genetic polymorphism identified between the species.