Objective To characterize the occurrence of Enterobacteriaceae and Cronobacter spp. in the powdered infant formula factories with dry-mix process, and study the potential contamination routes of Cronobacter spp. Methods Raw materials, intermediate products, end products, and environment samples from four factories were surveyed. Enterobacteriaceae and Cronobacter spp. were detected using traditional culture method. The isolates of Cronobacter spp. were profiled by pulsed-field gel electrophoresis(PFGE). Results The occurrence rate of Enterobacteriaceae was about 20% for the samples from the ground, air conditioning outlet and used cleaning tools. The occurrence rates of Cronobacter spp.were 2.56%(12/468)and 0.27%(6/2 185)from the product related samples and environmental samples in cleaning work area respectively. Clonal analysis using PFGE divided 22 Cronobacter spp. isolates into 13 patterns, each clone was unique to each factory and only four patterns were homologous respectively. The main source of Cronobacter spp. in end products was raw material, followed by environmental colonization strains. Conclusion It would help to get the distribution of Enterobacteriaceae and Cronobacter spp. in the powdered infant formula factories, identify the potential sources of Cronobacter spp. in the end products, develop sanitary control measures of the production process and ensure the end product safety.