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Polygonatum cyrtonema Hua, a rhizome‐propagating herb endemic to China, is used in many traditional Chinese medicines and foods. The hilly mountains in western and southern Anhui province is one of its main natural distribution and artificial cultivation areas. We assessed the genetic diversity and structure of P. cyrtonema germplasm resources in Anhui by nine pairs of SSR primers and selected morphological characters. The results showed that the 13 sampled populations of P. cyrtonema possessed normal levels of genetic diversity but could be clustered into three distinct genetic groups. The levels of within‐group genetic diversity was similar among the three groups, but their distribution areas and morphological characters were remarkably different. Group I was confined to the Tianmu (including Jiuhua) Mountains, group II was distributed in the Huangshan Mountains, and group III was restricted to the Dabie Mountains. Furthermore, the leaf length:width ratio significantly differed among groups, and the peduncle length of group I was significantly shorter than that of the other two groups. Levels of genetic differentiation among the three groups was close to that between different species within the genus. Thus, the three genetic groups of P. cyrtonema should be considered as independent units for conservation and breeding management in the Anhui region.

The taxonomy, distribution, horticultural value and cultivation requirements of the Chinese Polygonatum cyrtonema Hua (Convallariaceae) are discussed; illustrations and a full description are provided.