Abstract:[Objective] In order to understand the diversity and succession change of endophytic fungal communities of Aloe barbadensis at different habitats. [Methods] Healthy perennial samples were collected in Yunnan, Sichuan, Guangdong and Shaanxi provinces. The endophytic fungi were isolated from the foliage and roots of the samples. Then they were identified based on morphological and molecular methods. And the endophytic fungal communities were analyzed by statistical?evaluation. [Results] A total of 1 442 isolates were obtained which were belonged to twenty-nine different genera. Among which 96.88% only been observed to produce asexual or no spores, others were belonged to Ascomycotina (0.83%), Basidiomycotina (0.07%) and Zygomycota (2.22%) respectively. The Alternaria (35.63%), Fusarium (12.69%) and Phomopsis (11.65%) were the dominant genera. [Conclusion] The community of endophytic fungi from Aloe barbadensis of Yunnan and that of Sichuan has the highest similarity (Cs=0.88), while the community similarity of Guangdong and that of Yunnan was the lowest (Cs=0.73). Alternaria, Fusarium and Rhizoctonia were the dominant genera in root, but Alternaria, Phomopsis and Phoma were the primary one in foliage. Additionally, the isolation rate of Hypomycetes was the highest (31.42%) in spring, but that of Coelomycetes (31.01%) was the highest in autumn.