Abstract:To evaluate the landraces of C. moschata in Hainan Island, their genetic diversity and relationship were analyzed by combining morphological characters and ISSR and SRAP molecular makers. The result of phenotypic variation showed that all the morphological characters, excepting for runner length, growth vigor, fruit stalk and pulp texture, were differential among 28 Hainan Island landraces of C. moschata with the mean CV of 34.88%, of which the fruit shape was the largest. and some characters have remarkable relationship; All landraces can be clustered into two groups mainly according to the leaf size, color and the shape of leaf tip. The genetic diversity among 28 Hainan Island landraces of C. moschata revealed by ISSR and SRAP were basically the same, with high level. The H and PPB for all tested cultivars was 0.1943 and 62.90% respectively with ISSR marker; And with SRAP marker, The H was 0.2258 and PPB was 61.50 %. Furthermore, the UPGMA clustering with ISSR and SRAP was similar, all the landraces were clustered into five groups. But the clustering with ISSR and SRAP had low relation to that by morphological characters. Combination result of SRAP and ISSR showed that the mean GS was 0.7741, the genetic relationship between H13 and H17 was the closest among the 28 landraces studied, and the furthest one was between H31 and H18. There were rich genetic diversities among the 28 landraces studied; ISSR and SRAP markers could be effective for analyzing the genetic diversity and relationship among Hainan Island landraces of C. moschata. The results in the present study will provide applicable guidance for protection and utilization of Hainan Island landraces in C. moschata.