Seaweeds, such as Sargassum thunbergii, are important hosts of endophytic fungi, which contribute significantly to the diversity of aquatic fungal communities and have attracted growing scientific interest. In this study, endophytic fungi were isolated from S. thunbergii, a brown alga commonly found in the intertidal zones of Korea. Samples were collected from Seogwipo and Buan. Based on morphological characteristics and phylogenetic analyses of the ITS, LSU, SSU, CaM, TUB2, and RPB2 gene regions, two fungal species previously unrecorded in Korea were identified: Palmiascoma acericola and Aspergillus clavatophorus. These findings expand our understanding of seaweed-associated endophytic fungal diversity in Korean coastal ecosystems.