Objective To study the molecular characterization of Cronobacter sakazakii(C.sakazakii) from infant foods. Methods The C.sakazakii isolates were characterized using antibiotic susceptibility tests and whole genome sequencing (WGS). BioNumerics software was used to analyze and assemble WGS data. Then, the multilocus sequence typing (MLST), core-genome multi-locus sequence typing (cgMLST), virulence genes profiles were performed using assembled genome sequences. The resistance genes profiles and antimicrobial susceptibility were investigated. Furthermore, STs of C.sakazakii in this study were compared with those from PubMLST database. Results In this study, nine C.sakazakii isolates were detected and subtyped into five STs. ST1 and ST64 were the predominant STs, which were also the predominant STs of C.sakazakii in PubMLST database. Three C.sakazakii isolates were found to carry the mcr-9 gene. However, all C.sakazakii isolates were sensitive to 12 antibiotics including polymyxin B and E. ST1, ST64 and ST458 carried gtrB in addition to the common virulence genes. The nine C.sakazakii isolates showed highly genomic diversity according to cgMLST results. Conclusion ST1 and ST64 were predominant STs in this study, which were also predominant STs in clinical isolates in PubMLST database. These results suggested the potential pathogenicity of C.sakazakii. Our data underscored the importance of continuous surveillance of C.sakazakii in infant foods for prevention of foodborne disease caused by C.sakazakii.