A large number of traditional herbal products from medicinal plants are available in local markets. However, the risk of fungal contamination especially toxigenic Aspergillus species, Aspergillus niger and Aspergillus flavus was potentially possible. Thus, this study targeted to investigate the prevalence of A. niger and A. flavus and the occurrence of genes encoding toxins, aflatoxins and ochratoxin A among the fungi using the molecular method in 33 herbal products randomly collected from local markets in Khon Kaen province, Thailand. Based on the identification using DNA sequences of the internal transcribed spacer region (ITS), there were two Aspergillus species, A. niger and A. flavus, with prevalence rates of 73.6% and 0.1% respectively. The genes related to aflatoxins and ochratoxin A were undetectable in all isolates. This study suggested the products were naturally contaminated with the fungi, but they were safe from the toxigenic A. niger and A. flavus.