In order to provide molecular foundation for identification of Cucurbita genus germplasm, in present study, the molecular fingerprints of88 accessions of Cucurbita genus includingC. pepo. L, C. moschata. L and C. maxima.L were mapped using SRAP (Sequence Related Amplified Polymorphism) molecular markers technology and DNAman software. The results are as follow: the genome DNA of 88 Cucurbita genus germplasm were amplified by 35 pairs of SRAP primers selected from 200 pairs of primers. 499 bands were got totally, of which 438 were polymorphic bands, and the rate of polymorphic bands reached as high as 87.8%. DNA fingerprints of all these 88 Cucurbita genus germplasm were well constructed according to the amplified bands, and a unique molecular ID card was mapped for each species so that it can be identified successfully. Furthermore, the primer E5EM8, which has the best polymorphism, can distinguish 72 Cucurbita genus accession thoroughly. All the 88 Cucurbita genus germplasm could be identified using 5 pairs of SRAP primers. The results also showed DNA fingerprints of Cucurbita genus germplasm can be constructed successfully by SRAP molecular markers technique. This study has significance on identifying the accessions, constructing molecular database and protecting cultivar patent of Cucurbita genus.