Abstract: Genetic relationship of 24 white flesh loquat germplasms was studied by ISSR technique. 16 primers which could produce clear and polymorphic bands were screened out from 89 ISSR random primers. 195 locis were detected, of which 153 were polymorphic and the polymorphic percentage was 78.46%. As analyzed by NTSYS-PC2.0, the genetic similarity ranged from 0.55-0.89.24 white-flesh loquat germplasms were grouped into three sub-cluster when the similar coefficient was 0.72. Rich genetic diversity of white-flesh loquat germplasm resources was detected at DNA level. in which relationship were not so obvious correlation with geographic origin. Most germplasm resources which came from the same geographic origin had close relationship, But some germplasm resources with different source regions were clustered in a group obviously. In addition, during the reserch we also found that 7 special bands could be reference mark of 6 Loquat cultivars identity. Some specific ISSR markers could identify Guifei, Xinbai No.1 and Xinbai No.8.