Abstract: 95 accessions of longan genetic resources and 1 lichi genetic resource were analyzed by RAPD with 18 arbitrary 10mer primers. A total of 197 DNA bands were amplified. On the average, one primer amplified 10.944 bands, the number of the band amplified by each primer ranged from 7 to 15. The polymorphic degree was up to 100%. The results showed polymorphism of longan germplasm was high. The genetic comparibility was Calculated by Euclidean distance method(ED), the cultivars of longan was analysed by UPGMA, dendrogram genetic comparibility was established. When D＝0.75, the 95 genetic resources of longan can be divided into two types (a type of longan from Chinese and a type of longan from Thailan), when D＝0.6, the 89 genetic resources of longan from Chinese can be divided into three types (a type of Honghezi, a type of Chuliang and Dongbi, a type of Fuyan and Wulongling), when the D＝0.4, the 89 genetic resources of longan from Chinese can be divided into eleven types. The results have the theorical meaning for the future research on longan’s inheritance and assortment.