The polymorphism and the genetic relationships among 32 genetic resources of genus Nelumbo from Korea, Japan, China, USA, India, Thailand and Gabong were thoroughly investigated and extensively examined using ISSR markers. Out of 103 loci detected overall, 94 were identified to be polymorphic with a rate of 91.2%. The genetic similarity matrix revealed a wide range of variability among the 32 accessions, spanning from 0.227 to 0.833. The study findings indicate that the Nelumbo accessions have a high genetic diversity, and accordingly carry a germplasm qualifying as good genetic resources for cross breeding. According to the clustering analysis, different subspecies, N. nucifera and N. lutea, were divided into independent groups and all of the N. nucifera accessions could be classified into five categories. Compared to RAPD analysis, ISSR method showed a clearer picture of polymorphism among the accessions and exhibited a definite distinction even among the subspecies. In this respect, ISSR analysis is considered to be more effective in differentiating the accessions and subspecies of the genus Nelumbo than RAPD test.