The morphological and karyological characteristics of 27 specimens of Apodemus agrarius (Pallas, 1771) from the European part of Turkey were studied in detail and compared with those in the literature in order to provide a wider perspective on the taxonomic status of Apodemus agrarius in Turkey. In all the samples examined, 2n = 48 karyotype was observed with FN = 56 and FNa = 54. The 2n = 48 karyotype includes three pairs of metacentric, one pair of submetacentric and 19 pairs of acrocentric autosomes. Of the sex chromosomes, the X is a large acrocentric and the Y is a small acrocentric. In addition, bacular characteristics, which are very important in the taxonomy of this species, were examined in samples from Turkish Thrace for the first time.