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We have analyzed the genetic diversity of 45 squash genotypes in Cucurbita maxima, C. moschata, C. pepo and uniden-tified Cucurbita spp. (noodle-squash) with molecular markers. The 45 squash accesions showed molecular variations of 87.5% inRAPD and 74.4% in AFLP, respectively, which allowed to group them into 3 clusters at the genetic similarity of 54%. Noodle-squashlines were grouped into the same cluster with C. pepo at 89% similarity level. Genetic similarities within individual sub-groups were97% in noodle-squashes, 96% in C. pepo, 98% in C. moschata, and 98% in C. maxima, respectively. Korean, Japanese, and Americannoodle-squashes were separately grouped at the similarity of 97%. Since there were no distinct molecular markers to distinguish thenoodle-squashes and C. pepo in our study, we suggest that the noodle-squash could be one of the different ecotypes of C. pepo. In theagronomic traits of the noodle-squashes and three Cucurbita spp., the noodle-squash showed closer to the C. pepo than the other twoCucurbita species. In inter-specific crosses with the noodle-squash, the noodle-squash/C. pepo showed higher fruit and seed settingthan the other cros combinations. These results will be helpful to the studies of squash breding programs.
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