Lotus is an aquatic perennial plant that has religious significance in Buddhism, Hinduism, and many other Asian cultures. This plant is one of the earliest domesticated crops with ornamental and edible varieties (seed production and rhizome production). We resequenced the genomes of 45 cultivated accessions selected from three cultivated groups of lotus, 22 accessions of wild sacred lotus, and 2 accessions of wild American lotus to >13× raw data coverage. We identified 25 million single nucleotide polymorphisms (SNPs) in lotus. Population analysis showed rhizome and seed lotus groups are monophyletic and genetically homogeneous, whereas flower lotus group is genetic heterogeneity. By using these population SNP data, we identified 1214 selected regions in seed lotus, 95 in rhizome lotus, and 37 in flower lotus. Some of the genes in these regions contributed to the essential domestication traits of lotus. The domestication history of lotus enhanced our knowledge of perennial aquatic crop evolution, and the dataset provided the basis for future genomics-enabled breeding.