Two parental varieties, L591 (G. hirsutum) with high yield and HD138 (G. barbadense) with good fiber quality were selected for this study. The differences in perfonuance of agronomic traits between two varieties were confirmed. The polymorphism between two parental lines was survey using 746 SSR markers, selected from different sources. In addition, 221 markers were showed polymorphism and yield at 29.62 percent. The high polymorphic level obtained for the primer groups BNL, CIR and NAU. According to the previous published cotton genetic map, the polymorphic SSR primers detected in this study were distributed throughout 26 chromosomes of allotetraploid cotton genome.