We investigated the biodiversity of endophytic fungi of Bolboschoenus planiculmis and Schoenoplectus triqueter in Korea. Twenty five of these host plants were collected from six sampling sites. Internal transcribed spacer analysis identified a total of eighty five isolates from the collected plants. The isolates comprised nineteen taxa; most of the isolates (92%) belonged to class Dothideomycetes, followed by Sordariomyetes (4.8%), Agaricomycetes (1.6%), and Eurotiomycetes (0.8%). The most prevalent fungus was Cladosporium perangustum in B. planiculmis and Macrospora scirpicola in S. triqueter. There are very few studies of endophytic fungi in halophytes and these have reported biodiversity patterns different from those of previous studies in Korea. Our results should provide useful information for future research in Korea.