Genetic diversity and multiple mitochondrial phylogroups of the red fox have been revealed from scattered locations in previous studies. There is a still lack of information about the genetic diversity and phylogeographic structure of the red fox in Asia Minor. We investigated the genetic diversity in the Turkish red fox using a part of the cytochrome b mitochondrial gene (375 bp), and attempted to evaluate the phylogeographic structure in various geographic ranges of the species with the use of sequences available from the GenBank from various geographic origins and our data. Bayesian and Network analyses of the cytochrome b sequences from Turkey and GenBank suggested that the red fox is divided into four main phylogroups. They are grouped accordingly: Group 1 (SW Anatolia, Turkey and Hokkaido, Japan), Group 2 (Eurasia and North America), Group 3 (only North America), and Group 4 (Vietnam). The majority of Turkish haplotypes grouped with those of Eurasia. Despite the great distance between the localities, two haplotypes from SW Anatolia, Turkey grouped with previously reported haplotypes from Hokkaido, Japan. The present study shows that the Turkish red fox is nested within two main phylogroups and exhibits a high genetic diversity.