Abstract: 【Objective】This study aimed to identify Polygonatum germplasm resources from Fujian based on phenotypic traits and inter-simple sequence repeat DNA polymorphism （ISSR） molecular markers and perform genetic diversity analysis， to provide a theoretical reference for identifying and breeding Polygonatum germplasm resources.【Method】A total of 305 Polygonatum germplasms collected from Fujian Province were identified and classified based on 19 phenotypic traits （ten quantitative and nine qualitative traits） to screen Polygonatum germplasms with large differences in phenotypic traits. Then the germplasms without different bands were deleted in the amplification results to identify Polygonatum germplasm resources from Fujian with obvious differences in both phenotypic traits and genetic backgrounds.【Result】Variation coefficients of the ten quantitative traits ranged from 27.17% to 89.05%， with the average of 52.77%； the highest variation coefficient was found in leaf width， and the lowest in leaf length. Shannon-Wiener diversity indexes of the ten quantitative traits were 6.10-8.59， with the average of 7.88； the highest Shannon-Wiener diversity index was found in leaf length， and the lowest in fruit diameter. Shannon-Wiener diversity indexes of the nine qualitative traits were 0.22-2.08， with the average of 0.80； and the order was leaf shape>rhizome morphology>leaf and stalk color>perianth color>fruit color>phyllotaxy>rhizome color>inflorescence=fruit type. Based on ten quantitative traits and seven qualitative traits， the 305 tested germplasms were divided into five major groups： Group Ⅰ consisted of 121 germplasms of Polygonatum cyrtonema， Group Ⅱ included 94 germplasms of Polygonatum filipes， Group Ⅲ comprised 9 germplasms of Polygonatum kingianum， Group Ⅳ contained 38 germplasms of Polygonatum alternicirrhosum， and Group Ⅴ encompassed 43 germplasms of Polygonatum arisanense. Using high-quality DNA from nine germplasms as templates， nine ISSR primers with clear amplification bands， good reproducibility， and high polymorphism were screened. A total of 171 bands were amplified， including 152 polymorphic bands， with an average polymorphism percentage of 98.99%. Among these， primer UBC855 yielded the highest number of amplified and polymorphic bands. Primer UBC855 was used to screen and identify 96 Polygonatum germplasms with high phenotypic trait differences. After excluding germplasms without distinct band differences， 60 Polygonatum germplasms from different regions of Fujian Province were obtained. Cluster analysis results showed that the 60 Polygonatum germplasms could be classified into five groups： Group Ⅰ included 25 Polygonatum cyrtonema germplasms； Group Ⅱ included 25 Polygonatum filipes germplasms； Group Ⅲ included one Polygonatum kingianum germplasm； Group Ⅳ included five Polygonatum alternicirrhosum germplasms； and Group Ⅴ included four Polygonatum arisanense germplasms.【Conclusion】The phenotypic traits and ISSR molecular markers can be applied to identify Polygonatum germplasm resources from Fujian Province. Leaf size， leaf number， pedicel length， plant height， fruit size， leaf shape， and leaf and stalk color are important phenotypic traits for identifying Polygonatum germplasm resources from Fujian Province. The ISSR primer UBC855 could reveal the genetic diversity of Polygonatum germplasm resources from Fujian Province. The combination of phenotypic traits and ISSR analysis enables a simpler and more efficient method for identifying and classifying Polygonatum germplasms from Fujian Province.