Objective Analyzing the genetic relationships of the main cultivated varieties of grapes can provide a basis for exploring excellent germplasm resources and parent selection.

Methods Seventy-seven grape germplasms resources were targeted for the genetic diversity and structure study by using SCoT markers, and the Structure 2.3.4 software was used to conduct population genetic structure analysis.

Results A total of 68 bands, of which 65 were polymorphic, were amplified by the 10 selected SCoT primers with an average of 6.8 bands per primer. The genetic similarity coefficient of the germplasms was 0.59-0.97. At the coefficient of 0.626, the cultivars were classified into two categories of Pop1 that contained 34 germplasms mostly European and American hybrids and Pop2 that consisted of 43 germplasms largely Eurasian varieties.

Conclusion The SCoT molecular markers can identify the genetic diversity of grope germplasm, and the research findings provide a reference for the analysis of the phylogenetic relationships of grape germplasm resources in Sichuan.