Atractylodes lancea (Thunb.) DC is a Chinese medicinal herb. The Maoshan mountain area is famous for producing the authentic medicinal herb of A. lancea. Volatile oils from A. lancea show antimicrobial activity and include the characteristic atractylone, SymbolbA@ -eudesmol, hinesol, and atractylodin. Because the active compositions are different, A. lancea samples from different places are divided into the Maoshan chemotype and the Hubei chemotype.To study the formation of the authentic medicinal herb, the endophytic fungal diversity of the two chemotypes of A. lancea was analyzed. Maoshan chemotype A. lancea (MA) and Hubei chemotype A. lancea (HA) were transplanted from each habitat and cultivated in the same environmental conditions. The leaves were selected, and endophytic fungi were isolated and identified during spring, summer, and autumn in 2011.The results indicated that plentiful fungal diversity was present in A. lancea. A total of 530 endophytic fungi were isolated from the leaves of A. lancea, with an isolation rate of 58.89%. All of the isolates were identified based on their morphological characteristics and molecular phylogeny; the isolates belonged to 20 genera. The species in Alternaria, Colletotrichum, and Guignardia were the predominant groups of fungi, and their relative isolation frequencies were 36.04%, 19.43%, and 9.62%, respectively, which were much greater than the isolation frequencies of other genera.The isolation rate (IR) of endophytic fungi from MA was 70.22%, and that from HA with 47.53%. The diversity index, which was determined by the Shannon-Wiener index (H'), revealed that the diversity of endophytic fungi in MA (H' = 2.16) is somehow higher than that in HA (H'= 1.83). Sorenson's similarity index between MA and HA was 0.67, which indicated that the community composition of endophytic fungi from the two types of A. lancea was different to some extent. The dominant genera of endophytic fungi in the two chemotypes of A. lancea showed basic similarities; these genera included Alternaria, Guignardia, and Colletotrichum. However, some genera were chemotype-specific. The MA-specific genera included Leptospora, Acremonium, and Septoria; the HA-specific genera included Beauveria, Verticillium, and Chaetomium.The diversity of endophytic fungi among different seasons presented certain successive patterns.The IR in summer was the highest (IR = 71.33%) and was followed by autumn (IR = 63.00%) and spring (IR = 42.33%). This suggested that the isolation of endophytic fungi increased from spring to summer and then declined slightly in autumn. The Shannon-Wiener index (H') indicated that greater endophytic fungal diversity was observed during summer (H' = 2.20) than spring (H' = 1.64) and autumn (H' = 1.88). With respect to seasonal factors, Sorenson's similarity index between spring and summer was 0.71, and that between summer and autumn was 0.76, while that between spring and autumn was 0.64. This indicated that there were some differences in the community composition of endophytic fungi among different seasons, but the differences were not significant. The dominant genera of endophytic fungi of A. lancea isolated in different seasons included Alternaria, Guignardia, and Colletotrichum; all of these genera were observed during every season, showing a wide seasonal distribution.The results of this study offer information about the differences in endophytic fungal diversity of two chemotypes of A. lancea under the same environmental conditions; these results also reveal seasonal variation in the endophytic fungi of A. lancea. Differences in the community composition of endophytic fungi between two chemotypes of A. lancea may have an important effect on the genuineness of the medicinal herb. These results are important for understanding the formation of the authentic medicinal herb of A. lancea.