Abstract: OBJECTIVE To investigate the thermoduric bacteria species and contamination in Ophiopogonis Radix and Genkwa Flos, explore the influence on the thermoduric bacteria by refrigerated storage. METHODS According to Chinese Pharmacopoeia (2015 edition), the amounts of the thermoduric bacteria were identified after different boiling bath time, and the species of thermoduric bacteria were identified by 16s rDNA gene sequence test system. To investigate the variation of the thermoduric bacteria by refrigerated storage at the same time. RESULTS By increasing the boiling bath time, the amounts of thermoduric bacteria were reduced. The thermoduric bacteria were still at high quantity even after 120 min boiling bath in Genkwa Flos, and after 48 h refrigerated storage, the amounts of thermoduric bacteria were significantly increased. The thermoduric bacteria were subtilis. CONCLUSION For safety pledge, it is recommended to control thermodurie bacteria in the Chinese herbal medicine, and pay attention to the microbial contamination of TCM decoction service.