Objective To study the relationship and molecular characteristics of a non-toxic ogawa serotype Vibrio cholerae food isolate with food and clinical isolates at home and abroad.Methods Quantitative polymerase chain reaction （qPCR） and high-throughput sequencing was applied to obtain virulent genes distribution and genome sequence. Bioinformatic methods were used to identify their multi-locus sequencing typing （MLST） types. One hundred and one isolates genomes were mapped to reference genome Vibrio cholerae N16961 to obtain the single nucletiode variant （SNV）. All alignment was applied to construct the evolutionary tree after removing recombination. Comparative genome analysis was applied to the genes presence and absence in food isolates and close strains.Results The food isolate was a cholera toxin negative and toxin-coregulated pilus positive （CNTP） strain of Vibrio cholerae. The MLST type was ST1480 which belonged to the same clonal complex of the ST75 CNTP strain prevalent in Hangzhou. It was in the branch of L3b.1 in the phylogenic tree， and highly homologous to clinical isolates in 2011 （HZ11-1， HZ11-2）. After removing the recombination， there were only 26 different SNVs.Conclusion The food isolate was highly close to the clones of the CNTP Vibrio cholerae L3b.1 branch in Hangzhou. The source of infection in the sporadic cases in Hangzhou may be related to the contamination of reptile so that the disinfection of its breeding sites and sales sites should be strengthen.