The wild boar (Sus scrofa L.) is distributed across most parts of Turkey, a major biogeographic crossroads connecting Southwest Asia and Southeast Europe. However, no information on genetic diversity and population structure of this species in Turkey is available. In this study, we report on mtDNA sequence variability and phylogenetic relationships among wild boars with variable external phenotypes from both its European (Turkish Thrace) and Asian (Anatolia) distributions in Turkey. Phylogenetic analyses of mtDNA D-loop sequences (413 bp) of 53 newly sequenced wild boars from different localities in Turkey and 432 wild boar sequences from various geographic origins downloaded from GenBank were performed to particularly compare the phylogeographic position of wild boars from the European part of the Turkish range with that of specimens from Anatolia and to explore a possible phylogeographic substructuring in Anatolia. Relatively high genetic diversity was found in the Turkish samples, with a total of 17 haplotypes. Phylogenetic analyses revealed partitioning of the currently found Turkish haplotypes into two haplogroups, which were, however, only partially concordant with the geographic origins of samples (central and southwestern Anatolia vs. Turkish Thrace and northeastern and southeastern Anatolia). A median-joining network grouped most Turkish haplotypes with those previously reported from the Near East, whereas the remaining two haplotypes were included in the European 1 haplogroup. The combined phylogenetic analysis of the currently obtained sequences and all sequences retrieved from GenBank supported the earlier findings of four major haplogroups. The present study will serve as a baseline for more comprehensive studies to understand phylogenetic relationships of wild boars in Turkey and the Near East.