In order to understand the genetic relationships among numerous materials of common wild rice in Hainan Province and explore representative samples, this study used 32 pairs of SSR markers to conduct genetic diversity analysis and core germplasm construction on 2038 samples of Hainan common wild rice from 11 different cities and counties in Hainan Province. The results showed that the average effective allele (Ne) was 2.479, the richness Shannon index (I) was 0.975, the Nei's gene diversity was 0.570, and the percentage of polymorphic loci was 91.78%, indicating that the genetic diversity of Hainan ordinary wild rice is very rich.There are differences in genetic diversity among Hainan common wild rice from different sources. Hainan common wild rice from Lingao has the highest genetic diversity, while Qionghai common wild rice has the lowest genetic diversity, and its variation is mainly concentrated within the population.192 core germplasm of Hainan common wild rice were constructed using population first and multiple clustering methods, accounting for 9.42% of the total resources (2038). The core germplasm of Hainan common wild rice represents the genetic diversity and specificity of the original germplasm, and provides materials for the effective utilization of Hainan common wild rice resources.