The genus Quercus L. is one of the most abundant and important genera of woody plants in the Northern Hemisphere as well as in Turkey. In the current study which is the most comprehensive study dealing with Turkish oaks, sequence variations of three noncoding regions (trnT((UGU))-L-(UAA) IGS, trnL((UAA))intron, trnL((UAA))-F-(GAA) IGS) of chloroplast DNA (cpDNA) were used for phylogeographic and phylogenetic analysis on 319 individuals representing 23 taxa (17 species). The trnT((UGU))-L-(UAA) region was found to be the most variable and parsimony informative region. Twenty-eight cpDNA haplotypes were identified based on 34 substitutions and 22 indels. High number of haplotypes and h(T) > v(T) observed in populations of oaks in Turkey indicated that the Anatolian Peninsula might have been a refugium at Glacial Periods. Phylogeographic construction and molecular variance analysis revealed that Quercus cpDNA haplotypes were geographically structured. Although local haplotype sharing among species from same infrageneric clades was common, levels of hybridization differ between species pairs. Haplotype analysis revealed four infrageneric clades, namely Section Quercus, Section Cerris and two clades corresponding to Section Ilex, namely "Ilex" and "Coccifera." Furthermore, a Section Cerris haplotype was detected in the Aegean members of Q. ilex and Q. coccifera. Section Ponticae was placed in the Section Quercus cluster. In contrast to the phylogenetic reconstructions based on the nuclear DNA sequence data, Group Ilex seems to be polyphyletic based on plastome phylogeny. Chloroplast phylogeny of oaks reflects the traces of recent and ancient introgression events during diversification of species. In addition to this, incomplete linkage sorting may also explain this polymorphic assemblage. Therefore, further investigation is required to clarify the cpDNA phylogeny of oaks, especially for Section Ilex.