Chloroplasts have originated from an endosymbiotic relationship of multi-cellular organisms with single-cellular cyanobacterium and their evolution allowed plants to photosynthesize and maintain life on Earth. As chloroplasts retained their own DNA and due to their characteristics, such as maternal inheritance and non-recombination in most Angiosperms, they make excellent molecular tools. Previous studies regarding European oaks (Quercus) have shown excessive chloroplast sharing between Q. robur and Q. petraea with no clear species delamination based on chloroplast genomes, assuming parallel chloroplast capture events during the recolonization of oaks from the refugia after the end of last glacial maximum (LGM) as the cause of this pattern. In this study, we aim to shed more light on the evolution of European oaks by looking at their chloroplast genomes. Using 69 chloroplast genes in a molecular dating analysis, we examine if the timing of the split among chloroplast lineages predates the LGM, while positive selection on 34 chloroplast genes is being tested as an ancillary factor of the observed low genetic diversity. The results reveal old splits among chloroplast haplotypes and younger splits within lineages, suggesting that chloroplast sharing already occurred prior to the LGM in some lineages and/or refugia. Selection analysis shows relaxed purifying selection for most of the genes, however, positive selection on ccsA and rbcl genes is found. Positive selection on the rbcl gene possibly related to the adaptive evolution of RuBisCo enzyme conceivably indicates a selective sweep as an additional interpretation of the limited genetic diversity between these species. Nevertheless, to fully explore these hypotheses the integration of nuclear genomes for the detection of introgression events is needed, while analysis on the protein level can further evaluate whether the replacements of positive selected amino acids are associated with environmental adaptations.