**5. Conclusions**

The fungal microbiomes in MOR and AOF were first investigated by DNA metabarcoding. The results highlight the effectiveness of the technique to analyze fungal diversity in CHMs and the need for the surveillance of marketed herbs to guarantee quality. This study provided an early warning for subsequent potential mycotoxin biosynthesis and can serve as a basis for the safe use of edible medicinal herbs.

**Supplementary Materials:** The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/foods11121748/s1, Table S1: Taxonomical classification of OTUs; Table S2: The species and relative abundance of potential toxigenic fungi in each sample.

**Author Contributions:** Conceptualization, X.P.; methodology, W.J., M.Y. and X.P.; validation, X.P.; formal analysis, W.J., M.G., J.Y. and X.P.; resources, X.C.; data curation, W.J. and X.C.; writing original draft, W.J. and X.C.; writing—review and editing, X.P.; funding acquisition, X.P. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by the National Key Research and Development Program of China (grant number 2019YFC1604701) and the CAMS Innovation Fund for Medical Sciences (CIFMS) (grant number 2021-I2M-1-071).

**Institutional Review Board Statement:** Not applicable.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** All related data and methods are presented in this paper. Additional inquiries should be addressed to the corresponding author.

**Conflicts of Interest:** The authors declare no conflict of interest.
