Pedunculate oak (Quercus robur L.) is a key forest tree species in Europe, valued for its ecological significance and economic importance. However, its genetic resources are increasingly threatened by climate change, habitat fragmentation, and anthropogenic pressures. This study assessed phenotypic variability among 11 natural populations from the Republic of Srpska (Bosnia and Herzegovina) and the Northern Serbia region (Autonomous Province of Vojvodina) to support conservation planning and sustainable genetic resource management. Ten leaf morphological traits were analyzed from ten trees per population. Variance components were estimated using two-way ANOVA, and multivariate differentiation was evaluated through principal component analysis, canonical discriminant analysis, and cluster analysis. All examined traits showed statistically significant variation both among and within populations. Size-related traits (blade length, leaf width, lobe width, sinus depth, and leaf area) defined the main axis of morphological differentiation, while venation traits and width of the principal lobe had the strongest discriminative power among populations. According to previous genetic studies, the populations of Kupinovo, Bački Monoštor, and Morović in Serbia have been recognized as priority units for conservation due to their high levels of genetic diversity and strong spatial representativeness within the species’ natural range, and their importance is further supported and confirmed by the results of the present study. Building upon these findings, the results of the present study identify the Lukavica population as the primary candidate for conservation in the Republic of Srpska, with the Ugljevik population representing a secondary priority. Their clear morphological differentiation and distinctive ecological characteristics further highlight their significance for safeguarding both neutral and adaptive genetic diversity of pedunculate oak.