We investigated the biodiversity of endophytic fungi in and Junipreus rigida from Mt. Baekryeonsan and Mt. Johangsan in Korea. In total, 59 isolates were discovered from 26 host plants and identified using sequences from the rDNA internal transcribed spacer (ITS) region. Twenty taxa of endophytic fungi were identified in this study; 62% of isolates belonged to Leotiomycetes, 34% belonged to Sordariomyetes, and 4% belonged to Agaricomycetes. Results confirmed three previously unreported endophytic fungi in Korea: , , and . Community analysis showed that the fungal diversity patterns of the samples from Mt Baekryeonsan and Mt. Johangsan are similar to those from previous studies and varied depending upon host and locality.