Water chestnut (TrapaL.) is a floating-leaved aquatic plant with high edible and medicinal value. In this study, we presented chromosome-level genome assemblies of cultivated large-seed speciesTrapa bicornisand its wild small-seed relativeTrapa incisaby using PacBio HiFi long reads and Hi-C technology. TheT. bicornisandT. incisaassemblies consisted of 479.90 Mb and 463.97 Mb contigs with N50 values of 13.52 Mb and 13.77 Mb, respectively, and repeat contents of 62.88% and 62.49%, respectively. A total of 33,306 and 33,315 protein-coding genes were predicted inT. bicornisandT. incisaassemblies, respectively. There were 159,232 structural variants affecting more than 11 thousand genes detected between the two genomes. The phylogenetic analysis indicated that the lineage leading toTrapawas diverged from the lineage toSonneratiaapproximately 23 million years ago. These two assemblies provide valuable resources for future evolutionary and functional genomic research and molecular breeding of water chestnut.