In Switzerland forest genetic resources are mainly maintained in situ in gene reserves. Criteria for the selection of gene reserves are outlined. Important basic information is the distribution of a species and ecological differentiation among growing sites. Mainly autochthonous populations are treated as gene reserves. Certain minimum sizes are required for gene reserves. The phenotypic appearance of forest trees is of minor importance for the selection of in situ gene reserves in Switzerland. Genetic inventories based on gene markers are routinely conducted in populations that are potentially suitable as gene reserves. In this paper, results of genetic inventories are compiled for Norway spruce (Picea abies), silver fir (Abies alba), oaks (Quercus spp.) und checker tree (Sorbus torminalis). In Switzerland these species harbour considerable genetic variation at isoenzyme gene loci. Contributions of single populations to total gene diversity are shown for Norway spruce, silver fir, and checker tree. The spatial variation of a cpDNA gene marker in Switzerland is described for oaks. Future research will concentrate on variation at gene markers and at adaptive traits as well as on the reproductive system of widespread and rare tree species. Selection of genetic resources must not rely exclusively on a single criterion based on variation patterns at marker loci. However, gene markers will continue to play a major role in the programme for the conservation of forest genetic resources in Switzerland.