Objective Whole genome sequencing and analysis was conducted on a Burkholderia gladiolus pv. cocovenenans strain, isolated from raw corn flour sample which caused family agglutinative bongkrekic acid poisoning. The genetic characteristics of its virulence and pathogenicity were analyzed as well. Methods Genomic DNA was extracted from DBJ isolate, the whole genome sequencing was carried out. Bioinformatics method were used to mine and analyze the data obtained from sequencing. Results Two independent chromosomes (G1 and G2) and one plasmid (P) were found in DBJ isolate. The lengths of the chromosomes and plasmid were about 4 Mb and 300 kb respectively. The GC content of the two chromosomes was both around 68.0%, and that of the plasmid was slightly lower at 63.0%. The bon gene cluster was found on chromosome G2. The phylogenetic analysis showed that DBJ isolate and UCD-UG_CHAPALOTE stain which was isolated from corn sample in Canada were in the same clade. Among 255 strains, 31 carrying bon gene cluster and they had obvious genetic evolutionary tendency. Conclusion The bon gene cluster was located on the chromosome of Burkholderia gladiolus pv. cocovenenans DBJ, and it was the main pathogenic gene causing food poisoning in human.