Forty-one endophytic fungi were isolated from stem and leaves of young shoots of sprouting stumps and seedlings of Eucalyptus globulus. Plectosphaera eucalypti was the main species colonizing seedlings, shoot stems, mature leaves and to a lesser extent, xylem. Cytospora spp. and Microsphaeropsis sp. appeared confined to the xylem and Coniella minima to seedling stems. Young and mature leaves also showed differences in fungal colonizers: the former were essentially infected by C. minima and the latter by P. eucalypti and Harknessia hawaiiensis. A correspondence analysis performed on all taxa from stem samples has revealed three distinct clusters, corresponding to seedling, shoot xylem and complete shoot stems, respectively. Percentages of minimal similarity indexes among populations from xylem, complete sprouting stem and seedling stem were very low which also demonstrated tissue-specific differences in the composition of fungal endophyte populations. Several isolates of basidiomycetes with positive oxidative extracellular enzymes were present in all three stem units. They also overgrew and replaced the more frequent endophytes under laboratory conditions.