A comprehensive population was built by 15 cotton hybrids from Yangtze Rive basin through mixed polen pollination. 29 elite lines were derived by conventional selection in breeding nursery. The percentage of seed-cotton yield before frost showed the greatest variation among 12 investigated traits in field experiment, and then the seed-cotton yield and yield components, but there was little variation in fiber quality traits. The first 5 principal components were fiber quality, seed-cotton yield and and its components, maturity, lint percentage, and plant height with the contribution rate of 24.31%、19.67%、13.29%、10.81%、9.09% respectively by principal component analysis. Majority elite lines were clustered in the same group based on SSR molecular markers, which was distinguished from the varieties from Yellow River basin, showing narrow genetic background.