The fingerprinting and genetic relationship of 18 loquat(Eriobotrya japonica) cultivars, as well as the newlybred lines were characterized by ISSR markers to explore the appraisal method of loquat germplasms. Fifteen selected ISSR primers were used for PCR amplification. The results showed that, a total of 172 bands with distinct and good repeatability were scored, among which 157 were polymorphic, and polymorphic rate was up to 91.3%. All of the tested cultivars (lines) might be highly distinguished by ISSR markers generated by combinations of primers 825, 834 and 848. The genetic relationships of the tested genotypes were unraveled using UPGMA method based on the coefficient computed with ISSR markers, and two groups were obtained from dendrogram taking 0.60 as a threshold. Therefore, ISSR markers may be effectively employed to genotype the loquat germplasms, as well as to elucidate their genetic relationships.