Abstract: Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular markers were used to detect the genetic diversity among 13 Cucurbita ficifolia resources from 6 prefecture of Yunnan．The results showed that 43 and 41 bands were obtained by RAPD and ISSR markers amplified through 6 selected primers respectively．The PPB (percentage of polymorphic bands) in RAPD detection (90.70％ ) was higher than that in ISSR (51.21％)．The similarity coeficient ranging from 0.340 to 0.895 and from 0.162 to 0.941 respectively, and the ISSR (mean value of GS was 0.481) was more efficient than RAPD (mean value of GS was 0.698)．The germplasms were divided into three main cluster groups and five inferior groups by RAPD, and it also could be divided into four main cluster groups and six inferior groups by ISSR．The significant correlation between RAPD and ISSR markers was observed(r=0.536)．The dendrogram was constructed by UPGMA method could provide theoretical basis for Cucurbita ficifolia introduction culture or cross breeding in future.