Abstract: Identification and genetic diversity analysis based on ISSR marker for 19 germplasms of Polygonatum were conducted. The results were as follows. (1) Based upon the morphological characteristics of the plants, germplasms No. 1, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 18, and 19 were determined to be P. cyrtonema Hua; and No. 2, 3, 4, 5, 14, and 17, P. filipes Merr. (2) From the 100 primers isolated, 11 were amplified to render 170 distinctive and polymorphic bands with sizes ranging from 250 bp to 200 0 bp. (3) Using Popgen 32 software, an abundant genetic diversity was found to exist among these germplasms with similarity coefficients ranging from 0.604 9 to 0.824 4, and genetic distances from 0.193 1 to 0.502 7; and, No. 6 and 7 were closely related, while the No. 10 and 17 differed the most. (4) The UPGMA cluster analysis classified the germplasms into 2 groups and 4 subgroups with all P. cyrtonema Hua in Group Ⅰ and all P. filipes Merr. in Group Ⅱ. And, (5) as analyzed by Popgen 32, the genetic diversity of the 4 subclasses showed an effective number of alleles (Ne) to be 1.484 5, Nei's genetic diversity index (h), 0.292 3, Shannon diversity index (Ⅰ), 0.423 9, and total gene diversity (Ht), 0.413 2. It appeared that the current method based upon ISSR marker could be used to identify the individual species as well as show the genetic diversity and relationship among the species in the genus providing valuable molecular information for the introduction, acclimation, protection and utilization of the Polygonatum resources in the wild.