Abstract:In order to understand the genetic diversity of Alpinia oxyphylla in Guangdong, the genetic differences among 166 germplasms were studied by using SSR molecular markers. The results showed that a total of 88 alleles were detected by 14 pairs of SSR primers, and the effective alleles of each primer varied from 1.198 to 3.279 with an average of 2.599. The Shannon's information index ranged from 0.736 to 1.890 with an average of 1.107. The variance analysis showed that 20.87% of the variation came between groups. Based on principal component analysis and genetic structure analysis, the 166 germplasms could be divided into four groups, which did not show the regularity of morphological characteristics. Therefore, there were high genetic diversity mainly occurred within population, but the classification based on morphological traits and the clustering based on SSR molecular markers could not achieve the consistency.