Camellia hainanica, which is common in China’s Hainan Province, is an important woody olive tree species. Due to many years of geographic isolation, C. hainanica has not received the attention it deserves, which limits the exploitation of germplasm resources. Therefore, it is necessary to study population genetic characteristics for further utilization and conservation of C. hainanica. In this study, 96 individuals in six wild Camellia hainanica populations were used for ploidy analysis of the chromosome number, and the genetic diversity and population structure were investigated using 12 pairs of SSR primers. The results show complex ploidy differentiation in C. hainanica species. The ploidy of wild C. hainanica includes tetraploid, pentaploid, hexaploid, heptaploid, octoploid and decaploid species. Genetic analysis shows that genetic diversity and genetic differentiation among populations are low. Populations can be divided into two clusters based on their genetic structure, which matches their geographic location. Finally, to further maintain the genetic diversity of C. hainanica, ex-situ cultivation and in-situ management measures should be considered to protect it in the future.
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