[Objective] To study the structural diversity of the fungal communities on the surface of fresh citrus peel, with an aim to establish foundation for exploring the changes of the fungal community when the citrus peel became the citri reticulatae pericarpium (CRP) during storage and aging. [Methods] The fresh citrus peel from the Citrus cultivar –Citrus reticulata ‘Chachi’ and Citrus reticulata ‘Dahongpao’ was collected from 5 main citrus origins, namely, Guangdong, Sichuan, Guangxi, Jiangxi, and Chongqing. The fungal internal transcribed spacer (ITS) domain on the citrus peel surface was amplified on the Illumina HiSeq platform for high-throughout sequencing for the first time, the species annotations and abundance of the fungi were analyzed, and the structural composition of the fungal communities was analyzed based on the analysis of Alpha & Beta diversity. [Results] The effective sequences of the 8 citrus peel samples could be classified into 35 genera. The fungal communities on the citrus peel surface of cultivars like ‘Chachi’ and ‘Dahongpao’ with various origins were consistently made up of 7 genera, among which, Erythrobasidium, Penicillium, Aspergillus, Rhodotorula, Mycosphaerella were the top 5 genera in terms of the maximum relative abundance. In addition, it was the first time to discover Aureobasidium and Ramichloridium on citrus peel surface. [Conclusion] This research had determined the structural composition of the citrus peel surface fungal communities, which had established foundation for the correlation research on the fungal community changes and the quality changes of the crude medicine during the storage of citrus peel.