Water dropwort (Oenanthe sinensis Dunn, 2 n = 42) is a kind of aquatic vegetable rich in nutrients. Here, we present a high-quality assembly and analysis of the water dropwort genome. A total of 990.83 Mb genome assembly was anchored into 21 chromosomes using the combined technologies, including PacBio-CCS (HiFi), second generation Illumina sequencing, and Hi-C technologies. Obtained contig N50 length is 47.67 Mb. In total, 54,711 protein-coding genes in O. sinensis genome were annotated. In addition to the γ triplication event shared by eudicots, water dropwort underwent three rounds of whole-genome duplication (WGD) event. We characterized an additional polyploidization that occurred after the divergence of O. sinensis from the other three members of Apiaceae family, carrot, celery, and coriander, clarifying the chromosome evolutionary trajectory among these Apiaceae plants with known reference genome. WGD event have contributed to the expansion of gene families, including those with roles in cellulose and lignin biosynthesis. WGCNA analysis suggested that Os0507490.1 (OsG8H) played a potential role in cellulose and lignin metabolisms. The current data provided a valuable resource for accelerating molecular breeding programs of water dropwort and shed novel light on its genomic evolution, as well as the modulation of cellulose and lignin biosynthesis.