Abstract: In order to study the relationship of 95 accessions of squash germplasms and improve the efficiency of new varieties screening, 95 squash core collections were detected in polymorphism by using 150 pairs of SSR primers. The research showed that 32 pairs of SSR primers were effective to amplify clear and stable polymorphic markers among different squash core collections. These squash core collections were clustered by using Mega version 4.01. Results showed that genetic distance of 95 squash germplasms varied from 0 to 0.9412, the average genetic distance was 0.583, the total length of the branch SBL=10.3384. When the branch length was 0.39, 95 germplasms were divided into three groups by 32 higher polymorphic SSR primers. The first group was Cucurbita maxima, the second group was Cucurbita maschata, and the third group was Cucurbita pepo. This study provided scientific basis for germplasms evaluation, identification of germplasm resources and breeding of new varieties.