Abstract. Endophytic fungi were isolated from four healthy tissues (new leaf, old leaf, bark, and xylem) of three Japanese tea cultivars (Hokumei, Sayamakaori, and Yabukita) at the Saitama Tea Research Institute, Japan in July 2015. A total of 520 isolates was obtained from 600 segments and were classified into 44 fungal taxa; the majority (93.2%) belonged to the phylum Ascomycota. The lowest infection rate was found in the xylem tissue of all cultivars. The total infection rate did not differ significantly among the cultivars. Colletotrichum gloeosporioides f. sp. camelliae and Pleosporales sp. were the predominant endophytes in all tissue types and cultivars. Most of the dominant endophytes showed obvious cultivar and tissue preferences. Tissue type played a more important role in shaping community structure than did cultivar. Colletotrichum gloeosporioides f. sp. camelliae preferred bark and old leaf tissue while Pleosporales sp. preferred new leaf tissue. The colonization frequency of C. gloeosporioides f. sp. camelliae was significantly lower in the Yabukita cultivar. Stem tissues harbored more diverse endophytes than did leaf tissues.

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