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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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Summary To examine the effects of salicylic acid (SA), the ethylene precursor 1‐aminocyclopropan‐1‐carboxylic acid (ACC) and methyl jasmonate (MJ), which induce defence responses against pathogen in plants, on foliar endophytic fungi, we performed exogenous treatments of Quercus serrata leaves with these chemicals and subsequently isolated endophytic fungi. SA and ACC significantly reduced the isolation frequency of the most dominant fungus, a Xylaria species as identified by sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal DNA. In contrast, the frequency of the second most frequent fungus increased by SA and ACC. A few other fungi were also affected positively or negatively. Shannon diversity indices decreased by all treatments because of the uneven isolation frequencies of the endophytes. Our results imply that host defence responses induced by the chemical treatments reduced the number of infections of some endophytes while the frequency of some other endophytes increased benefiting from the reduction of competitors.