An overview of recent achievements and development of genomic resources in the Fagaceae is provided, with major emphasis on the genera Castanea and Quercus. The Fagaceae is a large plant family comprising more than 900 species belonging to 8-10 genera. Using a wide range of molecular markers, population genetics and gene diversity surveys were the focus of many studies during the past 20 years. This work set the stage for investigations in genomics beginning in the early 1990s and facilitated the application of genetic and quantitative trait loci mapping approaches. Transferability of markers across species and comparative mapping have indicated tight macrosynteny between Quercus and Castanea. Omic technologies were more recently developed and the corresponding resources are accessible via electronic and physical repositories (expressed sequence tag sequences, single-nucleotide polymorphisms, candidate genes, cDNA clones, bacterial artificial chromosome (BAC) libraries) that have been installed in North America and Europe. BAC libraries and physical maps were also constructed in Castanea and Quercus and provide the necessary resources for full nuclear genome sequencing projects that are currently under way in Castanea mollissima (Chinese chestnut) and Quercus robur (pedunculate oak).