To understand diversity and successional changes of endophytic Pestalotiopsis in plant communities, we completed surveys of endophytic Pestalotiopsis in plants belonging to the Fagaceae (10 species), Lauraceae (7 species), and Palmae (5 species) in the Botanical Garden of Guangxi Academy of Foresty Sciences. We identified 30 endophytic Pestalotiopsis species, of which 17, 19, and 17 endophytic Pestalotiopsis species were obtained from Fagaceae, Lauraceae and Palmae, respectively, with Pestalotiopsis microspora as the dominant species. We collected a total of 8, 12 and 12 endophytic Pestalotiopsis species from Cyclobalanopsis fleuryi (Fagaceae), Cinnamomum camphora (Lauraceae), and Arenga engleri (Palmae), respectively. We found the highest colonization frequency (6.67%) of Pestalotiopsis in Cinnamomum camphora. We also found that colonization frequencies of endophytic Pestalotiopsis were higher on twig tissues compared with leaf tissues for most plant species except Phoenix roebelenii. The total number of Pestalotiopsis species varied by season, with 18, 16, 12, and 10 endophytic Pestalotiopsis species collected in spring, summer, autumn, and winter, respectively. Colonization frequencies of endophytic Pestalotiopsis also varied by season with frequencies of 3.44%, 1.53%, 1.10% and 1.75% in spring, summer, autumn, and winter, respectively. This research showed that Pestalotiopsis had a preference for colonization in some plants and certain tissues, and its colonization frequencies fluctuated in different seasons.