As pine mushroom market size is about 800 billion won in the world, global trade is being increased. And in Korea, the import volume of Chinese pine mushroom is coming to maximum 10 billion won. Caused by this situation, quarantine on insect pests of pine mushroom was being important. For this problem, we tried to analyze DNA barcodes on Diptera inhabiting in pine mushroom. In this study, 253 fly individuals from Korean mushroom and 13 from Chinese one were used. Diversity on species level was analyzed based on 2.0% threshold approach. In a results, total of 23 species of six families were detected. Among them, 19 species of six families were found from Korean mushroom and four species were from Chinese one. Korean and Chinese faunistic compositions by DNA barcoding were quitely different from each other. Therefore, we consider that quarantine inspection on Diptera of pine mushroom is more reinforced, and monitoring on the diptera species from imported Chinese pine mushroom is needed.