Vibrio harveyi is an important pathogen for aquatic fish and invertebrates, that can lead to significant economic losses in the aquaculture industry. Rapid and accurate serotyping is essential for the diagnosis and epidemiological investigation of bacterial pathogens. In Vibrio spp., serotyping is based on lipopolysaccharide or capsule polysaccharide loci. In this study, we screened and extracted the location and full-length sequences of 12 different lipopolysaccharide biosynthesis loci from all available V. harveyi genome sequences from public database. Herein their gene composition, homology and variation are discussed, and a database is developed to rapidly type V. harveyi isolates based on differences in lipopolysaccharide loci. This study further analyzses the relationship between lipopolysaccharide loci and genome characteristics. The identification and characterization of these lipopolysaccharide loci could help researchers understand the genetic, molecular, and basis serotype structural specificity of this pathogen, and also provide opportunities for further development and improvement of the molecular serotyping method, which would aid the diagnosis and clinical treatment of the disease caused by this pathogen. •Identified the location and full length sequence of 12 different lipopolysaccharide biosynthesis loci for Vibrio harveyi.•Compared the gene composition, homologous and variation between these O-antigen encoding loci.•Developed a database which could be used to rapidly typing V. harveyi isolates based on the difference of lipopolysaccharide loci.•Analyzed the relationship between lipopolysaccharide synthesis loci and the genome characteristics.