Detailed phylogenetic relationships and molecular dating are still quite rare for the complex and diverse genus Salix L. Here we focus on the taxonomic status and phylogeny of twenty-six Salix taxa naturally found in Turkey using the chloroplast DNA regions (trn T-F, matK, and rbcL) to unravel the relationship among them. The status of Salix species was also checked in the phylogenetic tree constructed with the data from Internal Transcribed Spacer (ITS) region of nuclear gene, including 158 accessions from the GenBank and 126 newly generated sequences of 26 Salix taxa (24 species) naturally found in Turkey. The phylogenetic analysis of the sequence data from both the chloroplast (cpDNA) and nuclear (nrDNA) DNA regions enabled a reliable classification of the genus at the subgeneric level (Salix and Vetrix) with high posterior probability/ bootstrap values as 1/100. The study provides important information on the Salix phylogenetic placements and diverging times of S. pentandroides, S.apoda, S. armenorossica, S. pseudomedemii, S. pedicellata subsp. pedicellata, S. pseudodepressa, S. amplexicaulis, two subspecies of S.triandra, and two endemic species of Turkey (S. purpurea subsp. leucodermis and S. rizeensis) for the first time. Taxonomically, S. amplexicaulis and S. rizeensis previously classified under the subgenus Vetrix were clustered phylogenetically under the subgenus Salix. Subgenera Salix species appears to be diverged from the subg. Vetrix in Eocene (ca. 45.1 Mya) while the estimated divergence times of subg. Salix and subg. Vetrix dated back to 23.1 and 21.65 Mya, respectively. However, divergence times among species within Salix and Vetrix subgenera of Turkey seem to be around the Pliocene period. Molecular phylogenetic relationship between Salix species native to Turkey and Salix species from the world were mainly associated with taxonomic hierarchy, rather than geographic proximity.