Specialized metabolites contribute to plant defense against pathogens and herbivores, and to their protection against abiotic stresses (e.g. UV radiation, drought). In the context of global change, natural variation of these traits may become even more important to mitigate extreme climatic and biotic events and be a source of adaptive solutions in natural populations. Leaf specialized metabolites (LSM) were previously shown to be variable and to impact herbivore damage in populations of European white oaks. Here, we aim to describe the natural variation of LSM in sessile oaks across Europe and identify the underlying genetics to better understand the evolutionary forces shaping this variation. We sampled 225 individuals from nine provenances growing in a common garden in France and used high-throughput liquid chromatography coupled to non-targeted mass spectrometry to quantify 219 molecules. In addition, we performed whole genome sequencing of all individuals at low-coverage (~10X) to generate 1,4 millions markers (SNPs). We found that linkage disequilibrium decreased over 3 kb and that oak provenances displayed little genetic differentiation (pairwise FST<0.05). Genetic variation explained over 50% of the variation for 187 molecules and a genome-wide association study identify significant associations for 147 LSM. Overall, our results suggest that sessile oak provenances display extensive variation for LSM and that this variation has a very strong genetic component with many LSM having simple genetic architectures. On-going analyses of the signatures of natural selections and genes at these loci will help better understand the selective forces maintaining variation within provenances.