To determine the dominant fungal endophytes of the Japanese beech (Fagus crenata Blume) and to monitor their isolation frequency, we isolated fungi from symptomless organs of beech including leaves, petioles, and current and old (1- to 5-year-old) twigs after surface sterilization. Of the 13 fungal taxa obtained, 3 were isolated most often. An unidentified species of Discula and an unidentified sterile fungus, Lb, were isolated frequently from leaves, and an unidentified species of Phomopsis was isolated most frequently from twigs. The isolation frequency over the growing season varied for the two dominant fungal species in the leaves, Discula sp. and Lb. These two species had similar patterns of isolation, even in petioles and current-year twigs, although isolation frequencies of a given species varied with organs. An organ-specific distribution of the fungal species in the host plant was apparent. The three fungal species noted above were considered to be the dominant endophytes of the Japanese beech.Key words: fungal endophyte, Fagus crenata, isolation frequency, organ specificity.