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Water lily is an important ornamental flower plant which is capable of viviparous plantlet de-velopment. But there is no study reported to get insight into the molecular basis of viviparity in water lily. Hence, we performed a comparative transcriptome study between viviparous water lily Nymphaea micrantha and a non-viviparous species Nymphaea colorata at four developmental stages. The higher expression of highly conserved AUX/IAA, ARF, GH3 and SAUR gene families in N. micrantha compared to N. colorata is predicted to have a major impact on the development and evolution of viviparity in water lily. Likewise, differential regulation of hormone signaling, brassinosteroid, photosynthesis and energy related pathways in the two species provide clues of their involvement in viviparity phenomenon. This study revealed the complex mechanism of viv-iparity trait in water lily. The transcriptomic signatures identified are important basis for future breeding and research of viviparity in water lily and other plant species.