The rocky mouse, Apodemus mystacinus, is a rodent species distributed in the eastern Mediterranean region. This species lives in varied vegetation, including rocky and stony surfaces covered with forests, small bushes, or cultivated areas up to an elevation of 2700 m (Vohralik et al., 2002;Çolak et al., 2004). A. mystacinus has four controversial subspecies: A. m. mystacinus Danford and Alston (1877) from Sebil, Turkey; A. m. smyrnensis Thomas (1903) from western Turkey; A. m. rhodius Festa (1914) from Rhodes, Crete, and southwestern Turkey; and A. m. euxinus Allen (1915) from northern or northeastern Turkey. A. epimelas Nehring (1902), formerly described as a subspecies of A. mystacinus, is distributed in the Balkan region (former Yugoslavia, Greece, and Bulgaria). This subspecies has been raised to the level of species on the basis of morphometric studies using body size and dental characters (

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The bank vole, Myodes glareolus, lives in deciduous forests throughout the Palearctic region.

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The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.