Korea is representative of a country that consumes herbal medicines; most of the herbal medicines circulating in South Korea have been imported from developing countries in Southeast Asia, such as China and Indonesia. Recently, domestic hygiene and safety are issues that have come to the forefront, because herbal medicines currently in circulation could possibly contain contaminants or residues. Furthermore, the appearance or discovery of harmful new species due to environmental and industrial developments is becoming a social problem. Therefore, it may be necessary to consider and investigate these matters on a continual basis. Recently, mycotoxin contaminations in such foods as cereals, nuts, and powdered red pepper have been reported. They have become a problematic issue; the possibility of contamination in herbal medicines has also been considered. Nevertheless, recognition of and research into mycotoxin contamination in herbal medicines has been scarce because herbal medicine is used in only a few nations. In this research, we identified contamination by aflatoxin which is known to be the most potent mutagenic, carcinogenic, and teratogenic mycotoxin in Thujae Semen, a herbal medicine. We also found co-contaminations involving other mycotoxins, including ochratoxin A and zeraleanone.