Objective To trace the pathogenic cause of a foodborne disease outbreak case occurred in a primary school in Nanjing and analyze the pathogen characteristics and molecular epidemiological relationship, providing reference data for the source tracing and management of foodborne disease outbreaks. ?Methods A total of 47 foodborne disease outbreak related samples were collected. DNA nucleic acids of all the samples were extracted and performed by Real-time PCR to detect the foodborne pathogens and diarrheal viruses, while the routine bacterial isolation and culture methods were used to isolate and identify pathogenic bacteria. Drug susceptibility testing was conducted with the broth microdilution method. The isolated strains were subjected to whole genome sequencing (WGS) and further pathogenicity prediction and cogMLST analysis. Results Thirty samples were detected Cronobacter spp. nucleic acid positive, and all the other common foodborne pathogenic bacteria and diarrhea virus nucleic acids were negative. Nine Cronobacter spp. isolates (BQ1~BQ9) were obtained, including 6 anal swabs from patients, 2 anal swabs from the staff of the catering enterprise and 1 food retention sample. The drug resistance spectra of the 9 strains were basically the same. Online PathogenFinder predicted that all 9 strains have a high probability of pathogenicity. MLST typing showed 5 different ST types, and the BQ3, BQ4 and BQ9 strains belong to ST8 type. The cogMLST analysis found that BQ3 isolated from a patient anal swab and BQ9 isolated from a food retention sample were clustered tightly, and performed only 2 ST sites differences, indicating these two isolate were highly homologous. Conclusion Cronobacter spp. strains were isolated from this foodborne disease outbreak case and molecular epidemiological analysis showed that the strains from food retention sample and one patient anal swab were highly homologous. Although Cronobacter spp. is generally considered to be an opportunistic pathogen affecting infants and immunocompromised populations, the data from this study suggest that Cronobacter spp. has a high potential as a causative agent of acute gastroenteritis in healthy adults and adolescents, and its risk in foodborne diseases needs to be reevaluated. It is necessary to strengthen the surveillance of Cronobacter spp. in people with foodborne disease and foods other than infant milk powder and complementary foods.