The history of rice cultivation in Zhejiang Province is long-standing, with a rich of rice germplasm resources. At present, there are more than 2000 rice germplasm resources from Zhejiang Province in the National Rice Germplasm Resources Intermediate Bank (Hangzhou). However, these resources have not been systematically screened and identified, which may lead to the existence of some duplicated resources. Here, 1970 rice germplasm resources originating from Zhejiang Province have been used for genome variation map construction through the whole-genome resequencing. 10,532 core SNP markers were screened for genetic similarity calculation by SNP filtering based on sequencing depth, linkage disequilibrium, and missing rate. In this study, the analysis of 13 groups of main homonymous rice resources demonstrated that the genetic similarity among these homonymous rice resources was less than 95%. Moreover, the homonymous rice resources exhibited large phenotypic variations and were actually different rice resources. At the same time, pairwise genetic similarity of 1970 rice resources was calculated by using the core SNP markers, and 13 group rice resources combinations with high genetic similarity were selected. By comparing the phenotypic identification results and plant morphological characteristics, it was found that the rice resources with high genetic similarity had highly similar phenotypes and field performances, which confirmed the effectiveness of genetic similarity in rice resources identification to some extent. This study has essentially clarified the inventory of rice germplasm resources in Zhejiang Province, providing an important scientific basis for the conservation and utilization of rice germplasm resources in Zhejiang Province.