Abstract: In order to determine the differences in structure and optimum isolation conditions of Glycyrrhiza uralensis endophytes from different habitats, plate-separation method was used to identify endophytes in G. uralensis from Gansu, Ningxia, Inner Mongolia, Xinjiang, and Beijing. The isolation parameters were defined by investigating various concentrations and sterilization time of NaClO solution. The strains were identified by morphological and molecular biological methods. The results showed that 5% NaClO solution and sterilization time of 5 min were the optimal surface sterilization conditions. Among 129 strains of G. uralensis from 5 producing areas, 438 strains of endophytic fungi were isolated and belonged to 5 orders, 7 genera, and 11 species. Among them, 4 taxa were firstly isolated from the licorice in China. Fusarium was a common genus among the 5 regions. There were differences in the composition and structure of the endophytic fungi of G. uralensis from different habitats. Diversity analysis showed that the endophytic fungi diversity in Gansu was the highest and that of Beijing was the lowest. The comprehensive analyses indicated that the endophytic fungi of G. uralensis are diverse, and there were differences among the number, composition and population of endophytic fungi in five producing areas of Gansu, Ningxia, Inner Mongolia, Xinjiang and Beijing.