A systematic survey of the endophytic assemblages of Quercus ilex in central Spain has been performed, with the goal of evaluating the importance of geographical and seasonal factors on these fungal communities. Four sampling sites were selected; one of them was sampled twice, in the spring and the autumn. The collected plant material consisted of bark, twigs and leaves from eight trees per site. Fungal strains were isolated with the use of a surface-sterilization method with sodium hypochlorite. A total of 2921 fungal strains grouped into 149 ‘species’ or morphological types were recovered. The 10 dominant species, with isolation frequencies >1.5%, were Pyrenochaeta sp., Periconiella anamorph of Biscogniauxia mediterranea (De Not.) Kuntze, Pseudonectria sp., Cryptosporiopsis quercina Petrak, Alternaria alternata (Fr:) Keissl., two undetermined coelomycetes, Penicillium funiculosum Thom, Diplodia mutila Fr. apud Mont. and Ascochyta sp. Medians of fungal species per tree were significantly different among the sampled sites. The isolation frequencies of the dominant species, as well as other less frequent species, were significantly dependent on the sampling site. The degree of endophytic infection and the diversity of fungal species were significantly higher in the spring. The frequencies of all dominant species at one of the sites depended significantly on the season, except for C. quercina, Acremonium sclerotigenum (F & V Moreau ex Valenta) Gams. and D. mutila. Cluster analysis of the whole endophytic mycoflora of the sampled trees suggested that the geographical factor affects the endophytic distribution patterns more significantly than the seasonal factor.