Abstract: Objective]Screening closely related traits of Xinjiang upland cotton cultivars resources goals and objectives of the molecular markers,excavated chain has important value in use of genes related to the source traits.[Method]The genome of 94 self-fertile cotton varieties in Xinjiang was analyzed by 54 SSR markers.[Result]Population structure analysis showed that 94 cotton materials could be divided into two groups and one mixed group.The association analysis showed that 36 SSR loci were (P<0.05 )associated with fiber quality and agronomic phenotype in GLM(Q)model,12 loci were associated with strength,4 loci were associated with fiber micronaire,13 loci were associated with fiber length,1 locus was associated with E-longation,4 loci were associated with boll weight,1 loci was associated with growth process,1 loci was associ-ated with lint percentage.[Conclusion]Principal component analysis and population structure analysis reflect the proximity of the phylogenetic relationship of cotton varieties in Xinjiang from different angles.On the whole,the genetic diversity of self-fertile variety is not rich enough,and at the molecular level the differ-ences are not great,which demonstrates that great effort should be made to broaden the genetic basis of breed-ing.