Sequencing signals of the biparentally inherited ITS marker and sequence matching of the chloroplast trnK intron, matK and rbcL gene of an Indian plant identified as Nymphaea alba var. rubra contradict its identity. Additional signals depicted in chromatograms of the ITS region and the exact match of the maternally inherited chloroplast DNA sequences suggest that the Indian material is a hybrid of N. alba and N. odorata. Molecular cloning techniques resulted in the isolation of ITS alleles from the putative hybrid with DNA sequences not exclusive of either of the parental species. Such allelic DNA sequences confirmed that hybridization between N. alba and N. odorata has occurred. Our DNA sequence analyses indicate this plant is an interspecific hybrid involving N. odorata as the maternal parent, and N. alba as the paternal parent.