Objective This study was to understand the whole genomic characteristics of a foodborne pathogen Burkholderia gladioli pv.cocovenenans strain Co14, and also to predict and analyze the biosynthesis genes of its virulence factors bongkrekic acid (BA) and toxoflavin (TF). Methods The whole genome sequencing of Co14 was sequenced by the third generation high-throughput sequencing technology (PacBio).The biosynthesis genes of BA and TF were predicted by BLAST in the whole genome sequences. Results Two independent closed circle chromosomes were found in the whole genome sequence of Co14. The lengths of the two chromosomes were 4.1 and 4.0 Mb and their GC contents were 67.82% and 68.32%, respectively. A 146 kb completed plasmid was found in the genome, which GC content was 63.25% and it encoded 149 genes. In the sequence of chromosomes 1, BA biosynthesis related gene cluster bonR1R2LJKFGABDEHIM and TF biosynthesis related gene cluster toxRABCDE were found. Conclusion The whole genome sequence of Co14 laid a genetic foundation for further study of the pathogenicity and virulence factor biosynthesis mechanisms of foodborne pathogen Burkholderia gladioli pv.cocovenenans.