Acomys cilicicus is a rodent species endemic to Turkey, with a highly restricted distribution. However, there have been doubts regarding its taxonomic validity as a distinct species. Previous studies investigating the phylogeny of A. cilicicus have been unable to provide conclusive data to address this validity issue, primarily due to their reliance on two specimens from a single locality. In this study, we expanded the sample size to include 16 specimens from 5 different localities and conducted sequencing of a mitochondrial DNA gene region (cyt-b). Initial analysis of genetic distances revealed a close relationship between cilicicus, minous, and nesiotes. To further explore the phylogenetic relationships, we incorporated additional mtDNA sequences from GenBank into our analysis, resulting in the construction of a phylogenetic tree. Our findings demonstrate that cilicicus forms a distinct clade, supporting its status as a separate species. Moreover, the cilicicus clade was identified as the sister clade of A. minous. By estimating the divergence time, we determined that cilicicus diverged from its closest relative, minous, approximately 170 thousand years ago. Additionally, based on our sequence data, we propose a hypothesis suggesting that cilicicus might have been introduced to Anatolia from Crete during the Lower Palaeolithic era. We further discussed the inferred migration pathways of the Mediterranean region based on clade formation and migration analysis.