Artículo de publicación ISIDespite the ubiquitous presence of fungal endophytes in woody plants, mechanisms underlying variation in foliar fungal endophyte communities are poorly understood. Given that endophytes in woody plants are predominantly horizontally transmitted, fungal endophyte colonization of foliar tissues is likely to be influenced by plant resistance traits. Here, we evaluated the association between leaf resistance traits and colonization and community composition of horizontally transmitted endophytes (HTE) in 10 dominant trees species in a temperate rainforest in Southern Chile. Because resistance traits might restrict colonization of HTE, it was hypothesized that host trees with similar leaf resistance traits would show similar HTE communities. We measured leaf traits with reported roles in plant resistance against pathogens and/or herbivores: cell wall polysaccharides, leaf toughness, flavonoids, anthocyanins, terpenoids and chitinases. We also determined variation in fungal read counts, number of operational taxonomic units (OTUs), diversity and community structure across tree species. Foliar fungal endophyte communities were characterized using Illumina MiSeq sequencing of tagged amplicons of the ITS1 region. Fungal read counts were significantly different among host trees, while number of OTUs and diversity were similar among them. Multivariate analyses showed that community composition of endophytic fungi significantly differed among hosts, and that variation in cell wall, flavonoids, anthocyanins and terpenoids was associated with differences in HTE communities. We found that host trees sharing leaf resistance traits harbour similar HTE communities. Fungal read counts decreased with increasing content of cell wall polysaccharides, while endophyte diversity decreased with increasing anthocyanin levels. Fungal read counts, in contrast, were positively associated with terpenoids. Additionally, culture‐based data indicated that some HTE strains inhibited the growth of the common fungal pathogen Botrytis cinerea. Synthesis. Overall, we found that leaf resistance traits may influence fungal endophyte colonization and community composition in tree species, likely through deterrent effects of structural and chemical traits. We suggest that endophytic fungi that overcome resistance traits might play a role in plant protection.