The increasing demand for climate-adapted seeds and planting material poses a challenge due to the limited availability, particularly for tree species such as oaks. National parks, known for their large-standing diversity and a wide range of habitats, can serve as valuable sources for identifying trees suitable for both the initiation of tree breeding and conservation strategies. This study aimed to identify valuable forest genetic resources of the Thayatal National Park in Austria by selecting potentially drought-tolerant phenotypes. For this purpose, we selected 404 mature trees of Quercus petraea (Matt.) Liebl. from eight populations growing on medium to dry sites in eight populations. Further, we characterized them for autochthony, genetic structure, genetic diversity using genetic markers (plastid- and nuclear-SSRs) and estimated their age. Finally, we applied wood core analysis to estimate tree response to historical drought events to identify the possible drought-tolerant phenotypes. The age of the trees ranged from 29 to 245 years (as of the year 2023). All Q. petraea trees were inhabiting a plastid haplotype 17a, autochthonous for this area. Nevertheless, the genetic structure estimated by ten nuSSRs revealed a pronounced structure in the dataset, largely caused by young trees exhibiting lower genetic diversity. A total of 85 elite potentially drought-tolerant trees were finally selected based on their morphological response (resistance, recovery ability, resilience, and relative resilience) to three historical drought events (1992–1994, 1947, 1917). The intrinsic water use efficiency and its difference (iWUE and DWiWUE), estimated by isotope analysis of δ13C of latewood in wet (1987) and dry (1994) years, did not correlate with any of the drought response traits (Rt, Rc, Rs, rRs). We discuss the further use of the selected oak trees for the establishment of seed stands and orchards to enhance seed production and the integration of other omics approaches, such as large-scale high-throughput plant phenotyping (HTPP) and transcriptomics, for in-depth analyses of drought tolerance of selected phenotypes.