[Objective] This study was to reveal the genetic characteristics of colored cotton varieties grown in Xinjiang. [Method] Five white upland and two white sea is- land cotton varieties were processed complete diallel crosses with five brown cotton varieties and five green cotton varieties respectively, constructing 96 F2 populations, and the population number of those in line with Mendel＇s law were counted. The individual fiber colors were statistically analyzed in each F2 generation. The cluster analysis was carried out to the parents based on their agronomic traits, and the SSR was used to analyze the genetic diversity of parents. [Result] Both green and brown fiber colors were determined by single nuclear gene; brown fiber color mainly presented dominant heredity, while green fiber color presented dominant, incomplete dominant or recessive heredity. The cluster analysis indicated that brown cotton vari- eties in Xinjiang had closer genetic relationships with Xinjiang-native upland cotton varieties than other upland cotton varieties in China, but distant from sea island cot- ton varieties; while green cotton varieties grown in Xinjiang showed distant genetic relationships with both native and other upland cotton varieties in China, and most distant from sea island varieties. SSR genetic diversity analysis of the parents showed that in all white/brown cross combinations, Xinluzao31 and Xincaimian11 showed the highest polymorphism while 293-ZM-2 and Xincaimian5 showed the low- est; in white/green cross combinations, Xinluzao31 and Green 85 showed the highest polymorphism while Xinluzao13 and Xingcaimian12 showed the lowest. [Conclusion] According to the genetic model and cluster analysis of colored cotton, the quality of cotton can be improved by hybridizing the colored cotton with Xinjiang native or in- land cotton varieties of China. This study provides germplasm resources and further study basis for the breeding of new colored cotton varieties, and materials to the fiber color gene mapping and cloning in futur
