Phenotypic traits and microscopic structures of rhizomes as key indicators for the identification of medicinal rhizome herbs. This study conducted observations on the phenotypic traits and microscopic characteristics of rhizomes of Polygonatum spp. germplasm resources from 29 different origins. The results indicated that there were significant vari?ations in phenotypic traits among Polygonatum spp. from different regions.Among them， the coefficient of variation of fresh weight was the highest （77.95%）， and that of chromaticity was the lowest （8.78%）. In the genetic diversity analysis， the bud diameter exhibited the highest genetic diversity index （2.0646）. Principal component analysis revealed high loading rates for yield-related trait indicators （0.879， 0.727， 0.857， 0.838， and 0.732， respectively）. Cluster analysis of rhizome phenotypic traits categorized the Polygonatum spp. germplasm resources into three distinct groups. Additionally， variations were observed in the microscopic structures， particularly in the vascular bundles and mucilage cells of the selected varieties. In conclusion， significant differences exist in both phenotypic traits and microscopic structures of Polygonatum spp. from different regions， providing a theoretical foundation for the screening and evaluation of the germplasm resources， as well as for the variety identification.