Endolichenic fungi are a subgroup of fungi that inhabit lichens without participating in lichen formation and display no signs of disease. These fungi hold significant biological, medical, and industrial potential. However, our understanding of the diversity and characteristics of endolichenic fungi, particularly in South Korea, remains limited. Therefore, this study aimed to explore the diversity of endolichenic fungi in South Korea using culture-dependent and metabarcoding approaches. We obtained c.a. 4,000 isolates from 53 lichens, which comprised 3 phyla, 11 classes, 27 orders, 51 families, 107 genera, and 313 species. Sordariomycetes was most abundant class in the culturable diversity, and Hypocreales and Xylariales were abundant at order level. In metabarcoding analysis, however, Dothideomycetes was most dominant class in lichens. In addition, Capnodiales and Pleosporales were dominant at order level. Considering that endolichenic fungi have great value as biological resources, the difference in diversity based on the two methods suggests that the endolichenic fungi have high potential as a reservoir for securing more biological resources.