Because the classification of Nymphaea in India has been reported to be confusing, molecular taxonomic revision of four Indian representatives of the genus namely N. nouchali, N. pubescens, N. rubra and N. tetragona based on ITS, trnK intron and matK gene is presented and discussed. Molecular evidence provided here is in disagreement about the taxonomic identity of one specimen of N. nouchali and indicated a probable misidentification of N. tetragona. Interestingly, sequence analysis revealed lack of or low sequence divergence between N. pubescens and N. rubra. Phylogenetic relationship among members of Nymphaea subg. Lows, represented by all known species viz. N. lotus, N. petersiana, N. pubescens and N. rubra was also conducted. Maximum parsimony analysis of the combined data matrix depicted two clades with N. petersiana and N. lotus forming one. N. pubescens and N. rubra representing the other. Bayesian inference showed N. petersiana as first branching, followed by N. lotus with N. pubescens and N. rubra emerging as a separate clade. The results indicated no close association between N. petersiana and N. nouchali, thereby, contradicting the morphology-based treatment of placing N. petersiana in synonymy under N. capensis and N. nouchali, respectively. (C) 2010 Elsevier B.V. All rights reserved.