Vibrio parahaemolyticus is associated with seafood, and its pathogenicity and antimicrobial resistance are closely related to lipid A. In V. parahaemolyticus, free lipid A species and complete lipopolysaccharide coexist but the reason is unknown. In Escherichia coli, this reaction to covert lipid A to the full-length lipopolysaccharide is catalyzed by a bifunctional 3-deoxy-D-manno-octulosonic acid (Kdo) transferase WaaA. In this study, a monofunctional Kdo transferase in V. parahaemolyticus encoded by VP_RS01035 was identified. When VP_RS01035 was deleted in V. parahaemolyticus ATCC33846, no full-length lipopolysaccharide was synthesized, but more free lipid A species were accumulated, and most of them were modified by phosphoethanolamine. When V. parahaemolyticus VP_RS01035 was overexpressed in a newly constructed E. coli waaA mutant WH001, and the full-length lipopolysaccharide was partially restored, suggesting that VP_RS01035 could replace waaA in E. coli. In addition, hexa-acylated lipid A and Kdo-lipid A species were directly extracted from WH001/pB2-RS01035, suggesting that V. parahaemolyticus VP_RS01035 is monofunctional and less efficient than E. coli WaaA. These results indicate that lipid A biosynthesis in V. parahaemolyticus can proceed without the addition of Kdo and V. parahaemolyticus VP_RS01035 plays an important role on lipid A diversity in V. parahaemolyticus.