61 pairs of polymorphic and good repeated SRAP primers were screened form 144 pairs and used to amplify genome DNA of bitter gourd by PCR.A total of 2078 DNA bands were amplified, 863 of which were polymorphic.The average number of polymorphic DNA bands amplified by each pair of primer was 14.15, the ratio of polymorphic bands was 42.11%. UPMGA method was used to make a cluster analysis, and result showed that the genetic similarity among 43 bitter gourd germplasm ranged from 0.50～0.95.They were divided into two groups with the similarity coefficient of 0.65.The first group is wild species and the second group is semi cultivated species and cultivated species.The second group was divided into five subgroups with the similarity coefficient of 0.80( L2).The L2 division reflects bitter gourd germplasm genetic diversity which has higher correlation to fruit characters, source or geographic distribution. The first subgroups was divided into four groups on the similarity coefficient 0.83, broadly divided into smooth bitter gourd, top bitter gourd, fine-edge and round-tumor of bitter gourd ,spiked tumor or bump bitter gourd. Classification results is closely related to whether to have rib, thickness of ridge, tumor size and color. Papilloma of bitter gourd is initially considered as a primitive type.