Abstract: Objective To investigate the incidence and its main pathogenic bacteria infection status of food-borne diarrhea and analyze their influencing factors in Yunnan province from 2012 to 2016. Me thods 1743 cases of food-borne diarrhea were collected, which were supervised from 11 hospitals covering from 2012 to 2016 years in Yunnan province.We gathered and tested the biological samples. Meanwhile, we analyzed the main pathogenic bacteria and their influencing factors. Re s ults 65 positive strains samples were checked out in 1743 cases of food-borne diarrhea positive samples, the positive rate was 3.73% (65/1743) . Salmonella and Shigella strains were the main pathogenic bacteria, the main suspect food was meat and its products, as well as fruits and their products. In this study, Professions, methods of processing and clinical diagnosis were considered as the main factors of main pathogenic microbe detectable rates of food-borne diarrhea cases in Yunnan province. Conclus ion We should carry out public health education widespreadly in nursery, scattered children, farmers and migrant workers, students and other special crowds, provide intervention measures, attach great importance to food processing, reduce the possible contamination of food during processing, improve the level of clinical diagnosis and treatment and the recognization ability of food-borne diseases, and propose targeted prevention and control measures.Thus, food-borne disease can be prevented and controlled effectively.