This study aimed to reveal intraspecific variations in two Dryomys species distributed in Türkiye, based on mitochondrial DNA cytochrome b gene sequences, and to discuss the factors driving these variations in the context of phylogeography and genetic species concepts. As a result of Maximum Likelihood, Bayesian Inference, and Network analyses, which included haplogroups or lineages from Italy, Russia, the Caucasus, and Iran identified in previous studies, along with Turkish haplotypes, three major clades (MC1, MC2, and MC3) were identified within Dryomys nitedula. These clades began to diverge evolutionarily in the middle of the Late Miocene (8.82 million years ago) and exhibit significant genetic differences from one another. The Turkish haplotypes were divided into five distinct lineages (N1–N5), each within five subclades (SC1–SC5), which were nested within these MCs. These lineages, their geographical distributions, and the subspecies defined in previous studies that correspond to these lineages are as follows: N1 from the Thrace region (Dryomys nitedula wingei), N2 from the Black Sea region (potentially a new subspecies), N3 from western and central Anatolia (Dryomys nitedula phrygius), N4 from northeastern Anatolia (Dryomys nitedula tichomirowi), and N5 from eastern Anatolia (Dryomys nitedula pictus). The N2 lineage, distributed in areas close to the coastal side of the Eastern Black Sea region and with a range close to both N3 (D. n. phrygius) and N4 (D. n. tichomirowi), exhibited high genetic differentiation from these two lineages and was a candidate to be treated as a new subspecies of Dryomys nitedula in Türkiye. The N5 lineage, which includes haplotypes from the distribution areas of the populations initially classified as Dryomys pictus and later as Dryomys nitedula pictus in previous studies, was found to be more closely related to Dryomys nitedula kurdistanicus from the Zagros Mountains than to D. n. pictus from the central regions of Iran. Combining the results of this study with previous research, it is clear that the D. nitedula lineages in Türkiye, along with haplogroups or subspecies in neighboring regions diverged between the middle Late Miocene and Middle Pleistocene. This divergence is believed to have been driven by climatic cycles and geomorphological processes that shaped the topography of their distribution range. The high genetic diversity observed in the lineages of Anatolia suggests that the region may have served as a glacial refuge for D. nitedula. Similarly to the processes and factors shaping the evolution of D. nitedula, Dryomys laniger was found to have diverged into two lineages, western (L1) and eastern (L2 or Dryomys anatolicus), within its distribution range during the Late Pliocene (2.94 Mya). To make a more accurate taxonomic assessment of D. laniger, a larger number of samples is needed, and the distribution limits should be more clearly defined.

A total of 134 Apodemus samples, whose genetic diagnoses had been previously conducted, were morphologically examined from 39 localities in Northern Anatolia, Thrace, Gökçeada, Bozcaada and the Marmara Island. The variation boundaries of dental variations in the distribution areas of five Apodemus species (Apodemus flavicollis, Apodemus witherbyi, Apodemus sylvaticus, Apodemus uralensis, Apodemus mystacinus) included in the research were determined. The defining morphological characters of Apodemus species, which have a complex taxonomic status, and their variations according to regions were identified using samples that had undergone genetic diagnoses. It was determined whether geographical barriers such as the Marmara Sea, the Bosphorus and the Dardanelles, Melet river, Çoruh river and Kızılırmak separate populations of species from each other. It was found that the Kızılırmak likely caused a divergence in A. mystacinus samples, the Bosphorus and the Dardanelles likely caused a divergence in A. flavicollis species. However, it was not determined that the Melet river and Çoruh river caused a divergence within the species. Similarities and differences between island populations and mainland populations were identified in Apodemus species with distribution on islands. The differences observed in the Eastern-Western transition in Northern Anatolia were determined within the species and associated with habitats.