To estimate genetic variation in rhizome lotus(Nelumbo nucifera Gaertn.ssp.nucifera) germplasms in China,a total of 94 rhizome lotus germplasms collected from 18 provinces in China were assessed.The RAPD(randomly amplified polymorphic DNA) marker was employed.The selected 17 random primers detected 139 polymorphic alleles out of a total 207(67.15%).Nei’s gene diversity statistics and region differentiation parameters indicated that all germplasms had a relatively high level of genetic diversity with ne = 1.3202,h = 0.1937,I = 0.2982 and the gene flow among all regions was Nm = 5.5742.The UPGMA dendrogram clustered all 94 germplasms into two clusters:One contained eight commercial cultivars and major landraces,and the other included the wild and some special landraces from five regions,and the PCA analysis exhibited the similar result.Those germplasms from southwestern and eastern China had higher genetic diversity than those from the southern,northern and central China.Predominant proportion of genetic variation(95.61%) was found significant within rather than among(4.39%) regions,as revealed by AMOVA analysis.The data analysis also revealed that the genetic diversity of rhizome lotus germplasms among different regions is positively related to their geographic distances,though it is ambiguous to find the trend from the UPGMA dendrogram and the PCA analysis.A relatively high genetic diversity and gene flow resided in the root lotus germplasms;about 96% of the variation was found within region;accessions from southwest and eastern China have higher genetic diversity than those from the southern,northern and central China. To estimate genetic variation in rhizome lotus (Nelumbo nucifera Gaertn.ssp.nucifera) germplasms in China, a total of 94 rhizome lotus germplasms collected from 18 provinces in China were assessed. The RAPD (randomly amplified polymorphic DNA) marker was employed. Nei’s gene diversity statistics and region differentiation parameters indicated that all all germplasms had a relatively high level of genetic diversity with ne = 1.3202, h = 0.1937, I = 0.2982 and the gene flow among all regions was Nm = 5.5742. The UPGMA dendrogram clustered all 94 germplasms into two clusters: One contained eight commercial cultivars and major landraces, and the other included the wild and some special landraces from five regions, and the PCA analysis exhibition the similar result.Those germplasms from southwestern and eastern China had higher genetic diversity than those from the southern, northern and central China. Predominant prop ortion of genetic variation (95.61%) was found significant within rather than among (4.39%) regions, as revealed by AMOVA analysis. data analysis also revealed that the genetic diversity of rhizome lotus germplasms among different regions is related related to their geographic distances , though it is ambiguous to find the trend from the UPGMA dendrogram and the PCA analysis. A relatively high genetic diversity and gene flow resided in the root lotus germplasms; about 96% of the variation was found within region; accessions from southwest and eastern China have higher genetic diversity than those from the southern, northern and central China.