Objective The four pathogens isolated from two outbreaks caused by fermented corn flour products in Yunnan Province were identified by recA partial sequence analysis. Methods The four isolates were already identified as Burkholderia spp. on the basis of 16S rRNA sequence analysis. They were amplified by recA specific primers in polymerase chain reaction together with Burkholderia gladioli (CICC 10574). The products were sequenced. The sequences were blasted with 73 species in Burkholderia genus and a phylogenetic tree was constructed. Results Comparative analysis of genetic relationship of recA gene could identify and classify the 73 species of Burkholderia, even subspecies of B.gladioli. Conclusion The four isolates from food poisoning cases could be identified as B.gladioli by recA sequence analysis. Their sequences were different from those of plant pathogens of B.gladioli with specific single nucleotide polymorphism(SNP), and was identified as Burkholderia gladioli pv.cocovenenans.