Abstract: The inter-simple sequence repeat(ISSR) method was applied to assess the genetic makeup of 17,including 6 new longan varieties.Out of the 30 ISSR primers,5 were selected for the analysis.Cluster analysis showed that the genetic similarity coefficients ranged from 0.75 to 0.93,and that the 17 cultivars could be clustered into 4 groups using a genetic similarity coefficient threshold of 0.785.These varieties could be satisfactorily distinguished by a single ISSR primer,py-9,and established their digital DNA fingerprints accordingly.The results provided an important basis for identifying new longan varieties,as well as evaluating and utilizing the germplasm resources.