Abstract: Genetic relationships and diversities of 28 ornamental pumpkin and gourd accessions were assessed by random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat(ISSR) molecular markers. The results showed that 89 and 93 amplification bands were obtained by 12 selected RAPD and 13 selected ISSR primers, respectively. The PPB (percentage of polymorphic bands) in ISSR detection (86% ) was higher than that in RAPD (82% ).The similarity coefficient ranging from 0.33 to 0.99 and from 0.31 to 0.99 respectively，and the ISSR (mean value of GS was 0.68) was more efficient than RAPD (mean value of GS was 0.73)．Using cluster analysis (UPGMA) based on those polymorphism mixture bands amplified with RAPD and ISSR primers, the 28 accessions were classified into three groups obviously related with fruit skin color and shape. Group Ⅰ included 15 accessions, which fruit shapes were oblate, ovoid, spherical or cylinder, and which fruit developmental traits were early or late maturation. Group Ⅱincluded 11 accessions, which fruit shapes were soup spoon, pear, oblate spheroid or crown, and which fruit developmental traits were early or middle maturation. Group Ⅲ included 2 accessions with the fruit traits of gourd shape and late maturation.