Random amplified polymorphic DNA（RAPD）and inter-simple sequence repeat（ISSR）molecular markers were used to detect the genetic diversity among 38 bitter gourd (Momordica charantia L.)．The results showed that 93 and 81 bands were obtained by RAPD and ISSR markers amplified through 10 selected primers respectively．The PPB（percentage of polymorphic bands）in ISSR detection（61.29%）was higher than that in RAPD（50.54%）．The similarity coefficient ranging from 0.287 to 1 and from 0.221 to 1 respectively，and the ISSR（mean value of GS was 0.672）was more efficient than RAPD（mean value of GS was 0.694）.The germplasms were divided into three main cluster groups and six inferior groups by RAPD，which was similarly with the phenotype classification of bitter gourd protuberance，and it also could be divided into three main cluster groups and seven inferior groups by ISSR，which was consistent with the color classification of bitter gourd．The significant correlation between RAPD and ISSR markers was observed（r=0.550）．Combining with two methods would more suitable for the analysis of genetic diversity，and the result was related to the phenotype classification and geographical distribution．