Objectives: This study presents observation of microorganism such as total aerobic bacteria, total fungus, E. coli, Pseudonomas aerugjnosa, Staphylococcus aureus, and Salmonella typhimurium in herbal decoction manufactured by Korean medical clinic. Methods: We examined to observe microorganism using the requirements for the experimental methods recommended by FDA. For the identification, we observed microscopic methods and carried out polymerase chain reaction (PCR) and DNA purification. The purified DNA samples were analyzed by DNA sequencer. As compared with NCBI database. the results were identified by sequences similarity. Results and conclusion: 26 (55%) of 46 decoctions observed positive for microbial test. 12 (46 %) of 26 positive decoctions exceed requirement of microbial limit test. These microbial colony identified genus of Bacillus using microscopic and DNA sequencing methods.