The Nelumbo Genome Database is a comprehensive genomics resource for sacred lotus (Nelumbo nucifera). It houses the most updated chromosome-level genome assembly, along with gene annotations, expression profiles, and coexpression networks from 11 tissues. The database integrates genetic variants (over 26.9 million SNPs and 4.1 million InDels) and phenotypic data from 88 lotus cultivars, including 62 newly sequenced. Users can access tools for BLAST, primer design, gene search, and genome browsing via GBrowse/JBrowse. All data are freely available to support research in population genetics, molecular breeding, and functional genomics in lotus.