Oil–tea camellia has a long history of cultivation and utilization, with a history of more than 2000 years. In China, it is the main woody oil crop with high economic value and a national resource with unique characteristics. Concurrently, it is also known as one of the four major woody oil crops in the world. However, the genetic background of Camellia drupifera Lour. on Hainan Island in China is still unclear, and there is a great lack of systematic genetic characterization, which seriously hinders the development and utilization of oil–tea camellia germplasm resources and genetic improvement on Hainan Island. To analyze the genetic diversity and kinship between C. drupifera and its related species, this study utilized SSR molecular marker technology to genotype 160 individuals from 23 populations. A total of 137 alleles were amplified from the 14 polymorphic primers, with an average of 9.786. The average number of effective alleles and that of Shannon’s information index for each locus were 1.865 and 0.633, respectively, suggesting that the screened SSR markers presented a moderately high level of polymorphism. Additionally, the mean observed heterozygosity (0.915) was greater than the mean expected heterozygosity (0.450), indicating an excess of heterozygotes in the tested population. The results of the principal component analysis (PCA), molecular variation analysis of variance (AMOVA) and population structure analysis were generally consistent; specifically, there was a high degree of individual heterozygosity within the population, and genetic variation occurred primarily among individuals within the population (90%) but rarely among groups (10%). Additionally, the UPGMA clustering divided the 160 germplasm resources into four major clades, and C. drupifera was principally grouped in two distinct branches; meanwhile, Camellia gauchowensis was also mainly clustered in these two clades. Camellia oleifera individuals were chiefly concentrated in other independent branches. It can be speculated that C. drupifera is genetically close to C. gauchowensis, but genetically distant from C. oleifera. This study can provide the scientific basis for the identification, collection, preservation, evaluation, and innovative utilization of oil–tea camellia.
