To investigate the community structure and diversity of endophytic fungi in the leaves of Artemisia argyi, leaf samples were collected from five A. argyi varieties grown in different cultivation areas in China, namely, Tangyin Beiai in Henan (BA), Qichun Qiai in Hubei (QA), Wanai in Nanyang in Henan (WA), Haiai in Ningbo in Zhejiang (HA), and Anguo Qiai in Anguo in Hebei (AQA), and analyzed using Illumina high-throughput sequencing technology. A total of 365,919 pairs of reads were obtained, and the number of operational taxonomic units for each sample was between 165 and 285. The alpha diversity of the QA and BA samples was higher, and a total of two phyla, eight classes, 12 orders, 15 families, and 16 genera were detected. At the genus level, significant differences were noted in the dominant genera among the samples, with three genera being shared in all the samples. The dominant genus in QA was Erythrobasidium, while that in AQA, HA, and BA was Sporobolomyces, and that in WA was Alternaria, reaching a proportion of 16.50%. These results showed that the fungal community structure and diversity in QA and BA were high. The endophytes are of great importance to the plants, especially for protection, phytohormone and other phytochemical production, and nutrition. Therefore, this study may be significant with the industrial perspective of Artemisia species.
