Objective To study the molecular characteristics and antibiotic resistance of Bacillus cereus(B.cereus ) from foods in Shanghai. Methods The B.cereus isolates were characterized using antibiotic susceptibility tests and whole genome sequencing (WGS). BioNumerics software was used to analyze and assemble WGS data. Then, multilocus sequence typing (MLST), virulence genes profiles and antibiotic resistant genes were analyzed using assembled genome sequences. The antimicrobial susceptibility was investigated. Furthermore, STs of B.cereus in this study were compared with those from PubMLST database. Results In this study, all 37 isolates were confirmed as B.cereus isolates. The 37 B.cereus were typed into 34 STs with 7 new STs. The result of STs showed high diversity. All 37 B.cereus isolates had nheA, nheB and nheC genes. The positive rate of hblACD genes was 37.8%. However, only 16.2% of B.cereus had ces genes. Furthermore, two ST26 B.cereus isolates with ces genes from ready-to-eat food were identified. The antibiotic resistance rate to Ampicillin, Penicillin and Oxacillin was high, which was not consistent with antibiotic resistant genes. Conclusion The STs of 37 B.cereus from food in Shanghai showed high genetic diversity, which suggested the molecular surveillance should be enhanced. Fundamental data can be obtained using whole genome sequencing for tracing B.cereus isolates and analyzing pathogenicity.