Abstract: Agarwood is a traditional medicinal material and natural fragrance in the world, with long history of application. At present, Aquilaria Lam. is the main species in agarwood production. The development of and market demand of agarwood industry has led to excessive exploitation and depletion of Aquilaria tree species in the wild, posing a threat to their germplasm diversity and sustainable development. To better utilize and protect the agarwood resources, this paper analyzed the development status of the agarwood industry based on the reference materials related to genetic diversity and molecular identification of Aquilaria, combined with the market research at home and abroad. And we conducted a systematic investigation into the development and utilization of the germplasm resources of Aquilaria in Guangdong, Hainan, Guangxi, Fujian and other domestic provinces as well as in overseas countries, such as Malaysia and Vietnam. We summarized and outlined the genetic diversity and molecular identification studies of Aquilaria plants at home and abroad. We explored the research progress of genetic diversity in Aquilaria from four aspects, including phenotypic traits, DNA molecular markers, DNA fingerprinting technology and nuclear genome level, and the current research status of molecular identification of Aquilaria from three major aspects, including DNA fingerprinting, DNA barcoding of nucleoplasmic gene fragments, and put forward the problems and trends of Aquilaria in molecular genetics, with a view to providing references for the researches of germplasm resources of Aquilaria.