Abstract: ObjectiveThe study aims to establish the DNA fingerprints and throw light on the genetic diversity of the Japonica Rice in Xinjiang.MethodThe Japonica Rice of 89 varieties were used as materials to analyze the genetic diversity and genetic relationship by 70 SSR markers.ResultThe result showed that there were 63 pairs of primers with polymorphic fragments and 388 effective alleles were detected.Namely, each pair had 6.158,7.The average polymorphism frequency index was 0.237,1 and the genetic similarity coefficient between the 89 materials was 0.72~0.88 with high similarity.If 0.73 was taken as a standard,all materials could be divided into 5 groups,but most were in one group.ConclusionHowever,generally speaking,the genetic background comparability was high and the diversity was low.It is demonstrated that the genetic basis of the Japonica Rice in Xinjiang is narrow.Therefore,identifying and making use of the new ge-netic resources and creating breeding materials should be strengthened.