Starch is one of the main components of lotus rhizome and seed, and has a high potential influence on their eating and processing quality. However, little is known about the molecular mechanism underlying starch synthesis in lotus plants. Here, we report a genomewide identification and characterization of genes encoding granule-bound starch synthase in sacred lotus. Two GBSS genes, designated NnGBSSII-1 and NnGBSSII-2, have been identified in the genome of lotus variety “China Antique.” NnGBSSII-1 is expressed in all tested tissues, including leaf, flower, leafstalk, rhizome, and seed, whereas NnGBSSII-2 is a pseudogene and its transcripts have not been detected in any tissues. Overall, the expression level of NnGBSSII-1 gene is positively correlated with amylose accumulation in lotus rhizome and seed. Moreover, a phylogenetic analysis shows that GBSS genes from N. nucifera and N. lutea are clustered together, and they have a closer relationship with GBSS genes from Proteaceae. This result supports the hypothesis that Nelumbo is taxonomically placed in the lotus family, Nelumbonaceae, under the order Proteales. Our results will be helpful for future genetic improvement of starch quality in rhizome and lotus seed.