This study investigated the phenotypic and genotypic characteristics of YN0303, an isolate from a food poisoning case occurred in Yunnan Province in 2003.Methods The strain was identified by 16S rDNA and 16S/23S rDNA ITS analysis, together with morphology, biochemical and gene analysis. Toxic gene profiles, panC analysis, mutilocus sequence typing and high performance liquid chromatography-mass spectrometry (HPLC-MS) analysis were further applied.Results YN0303 was confirmed to be Bacillus cereus. Although it's an isolate from a typical food poisoning case, it was negative for cereulide-producing related ces gene and no cereulide was detected in HPLC-MS quantitative analysis, while it was positive for entero-toxigenic genes such as hbl, nhe, and cytK2. It's also different from typical emetic B.cereus in biochemical tests. It belonged to cytotoxic IV group, while emetic strains should belong to Ⅲ group. YN0303 forms a new ST in mutilocus sequence typing analysis, which was an independent branch in phylogeny tree.Conclusion More than one B.cereus strain involved in this emetic food poisoning case, and YN0303 was not the main pathogenic strain. But as a cytotoxic strain, it might be involved in co-infection.