To investigate the status of the bacteria contamination in local characteristics foods in Yunnan Province. Methods The national standard methods about hygiene indexes and common foodborne pathogenic bacteria had been implemented in local characteristics foods from four representative city in Yunnan Province in 2013, and data were analyzed with SPSS 19.0 software. Results The unqualified hygiene indexes accounted 56.50% in 288 food sample of 10 types, while the pathogenic bacteria mainly from unpacked food accounted for pathogenic bacteria with an overall detection rate of 12.15%, Salmonella and Staphylococcus aureus was the major contaminant in cold pig skins and cold food with detection rates of 8.33% and 3.13%, respectively, Staphylococcus aureus had the highest of 31.25% for cold pig skin, followed by Yunnan goat cheese 25.00%, Bacillus cereus in cold food detection rate 7.81%, Shigella and diarrheogenic Escherichia coli were not. Salmonella and Staphylococcus aureus in all four quarters of 2013 were not different between detection rate. Conclusion Yunnan local characteristics foods with unpacked condition were found serious bacterial contamination, indicating hidden risk of foodborne diseases. Considering quite a proportion of the feeding, uncontrolled raw material sources, no cooked process, it is necessary to strengthe supervision of relevant food hygiene monitoring and management on food safety.