Specific DNA markers are useful for capability to identify Nymphaea subgenus Lotos level in subgenus and species. Ten sample with RAPD technique, and only 8 markers could amplify DNA and gave polymorphic bands. The genetic similarity based on these RAPD markers ranged 0.288-0.617, suggesting that these Nymphaea Lotos genotypes had genetically close relationship. The dendrogram using the UPGMA algorithm based on RAPD marker systems divided the 10 sample genotypes into tree main groups. Development of SCAR Markers tree pimers. Two primer (NYM001 and NYM004) nonspecific are useful for capability to synthesis anything. NYM003 primer specific on genus Nymphaea.