Objective To isolate and identify the pathogenic bacteria in the first food poisoning related to bongkrekic acid in Guangdong Province. Methods The pathogenic bacteria was isolated and identified according to GB/T 4789.29-2003 Microbiological Examination of Food Hygiene, Examination of Pseudomonas cocovenenans subsp. farino fermentans. Meanwhile, 16S rDNA sequence of the isolates were analyzed. Results In 31 related food samples, 28 strains of Burkholderia spp. were isolated, including Burkholderia gladiolo(15), Burkholderia cepacia(3), Burkholderia vietnamiensis(3)etc. By 16S rDNA sequencing, in vitro toxin-producing test and bongkrekic acid measuring, 14 Burkholderia gladiolo isolates were identified as specific pathovar in 3 food samples. Conclusion It suggests that Burkholderia gladiolo could be identified by biochemical test and 16S rDNA sequence analysis. The Burkholderia gladiolo pathovar which could produce bongkreic acid was responsible for food poisoning, combined with toxin production.