Objective To investigate the contamination and molecular typing characteristics of Cronobacter in infant food and formula powder in Wenzhou, to analyze the genetic relationship between different strains. Methods According to the national standard GB 4789.40-2010, Cronobacter was isolated and identified from food. Pulse field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to analysis the genotyping of Cronobacter. Results A total of 737 food samples were collected from 2013 to 2017, and the total detection rate of Cronobacter was 6.1% (45/737). The detection rate of infant formula rice flour was the highest, 23.4% (37/158). Totally 45 strains of Cronobacter were identified as C.sakazakii, C.malonaticus and C.muytjensii. Among them, C.sakazakii was the majority, accounting for 73.3%(33/45), followed by C.malonaticus of 24.4%(11/45). There were 25 ST types in 45 strains, and ST64, ST1, ST40, ST4 and ST7 were the dominant types. 45 strains of Cronobacter were divided into 38 clusters, and no obvious dominant cluster and aggregation were found. The result of PFGE and MLST showed that the majority of strains with the same PFGE type also had the same MLST type, but the same MLST type did not necessarily indicate a high genetic relationship. Conclusion The contamination level of Cronobacter was relatively low in foods of Wenzhou, among which the detection rate of infant formula rice flour was the highest. Cronobacter isolated from foods showed highly polymorphism and dispersion.