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Random amplified polymorphic DNA (RAPD) markers were used to analyze genetic variation of Podocarpus imbricatus in Hainan Island and Mainland of China. Two populations of Dacrydium pierrei were used as comparison materials. Both Podocarpus imbricatus and Dacrydium pierrei showed a low level of genetic diversity. However, Podocarpus imbricatus showed higher genetic diversity and higher population differentiation than Dacrydium pierrei. The geographic range may affect the genetic diversity of Podocarpus imbricatus and Dacrydium pierrei significantly. The UPGMA cluster tree showed that populations of Podocarpus imbricatus in Hainan Island and Guangxi Zhuang Autonomous Region were closer than those in Yunnan Province, indicating possible gene flow between Hainan Island and Guangxi Zhuang Autonomous Region. The young geological history of Hainan Island and the three times of unification and separation between Hainan Island and the Mainland may give the two species more possibilities of gene flow.