The focus of protected area establishment is shifting towards protected area networks as part of an "ecoregional" conservation approach. Protected areas can function as gene reserves if certain genetic criteria are considered. A methodology for selecting protected areas in the Mediterranean basin and its possible effects on the in situ conservation of gene resources of forest trees are presented in this paper. Due to special biological, social and biogeographical factors, which characterize forests in this region, the function of protected areas as in situ gene reserves has more advantages than disadvantages.