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Fungal endophytes inhabit healthy tissues of all terrestrial taxa studied to date; however, fungi associated with woody tissue have been frequently overlooked. Here, we examined endophytes associated with healthy living stems of tree species exotic to Argentina (Broussonetia papyrifera, Celtis occidentalis and Ligustrum lucidum) in a natural reserve. To achieve this objective, fungi were induced to develop within the wood by drying sections of branches. For comparison purposes, a study of the organisms present on superficial and inner bark was carried out. Fifty-seven strains belonging to 12 different taxa, dominated by the anamorphic states of ascomycetes, were obtained from the 180 cultured chips. Coprinellus micaceus, Lecythophora hoffmannii and Rhizopus microsporus are cited for the first time as endophytes. Only two taxa appeared on more than one tree species. Assemblages of fungi obtained from each tree species were different and the fungal endophytes isolated were very different from those previously recorded for leaves of the same hosts in the same area. Thus, it is probable that the endophytes exhibit host- and tissue-specificity. Considering three main factors: 1. the invasive nature of two of the selected hosts, 2. the evaluation of woody tissue and 3. the taxonomic identity of the fungal isolations, hypotheses concerning ecological implications are here discussed. In this sense, Broussonetia papyrifera and Ligustrum lucidum could be considered as sources of potential inoculum for native plants, especially in protected areas, and the high diversity of fungal species living within the tissues of the hosts studied suggests their potential as important fungal reservoirs to be taken into account in conservation issues.