Collectively, our results characterize the structure, evolutionary, and some functional features of the lotus TPS gene family. Based on systematic analysis of lotus genomes, we identified 9 TPS genes. Gene structure analysis showed that NNU_022788 might be the ancestral member, from which other genes were derived. Regions outside the TPS domain in nine NnTPS genes evolved faster than regions within the TPS domains. Based on phylogenetic tree constructed using TPS genes from lotus, Arabidopsis, polar, soybean, and rice, TPS genes could be classified into two main subfamilies (I-II). Lotus TPS genes showed species-specific expanded manner. Three amino acid residues (669, 704, and 753) in TPP domain were identified as the most important residues for the functional divergence of these TPS genes. Moreover, 2 groups (group I-1 and II-2) were believed to have undergone positive selection based on likelihood ratio test. Expression pattern analysis showed that NnTPS genes might mainly have function in sink tissues and two NnTPS genes (including NNU_014679 and NNU_022788) might play important roles in lotus energy metabolism and stress responses.