We collected one specimen of Apodemus speciosus with small eyes suggestive of a microphthalmia-like aberration in Fujisawa, Kanagawa Pref., Japan. The external appearance and skull characteristics of this specimen were normal except for the eyes. We observed under the microscope that there was a small lens-like tissue and soft tissue in the internal status of the eye. In contrast, a normal specimen’s eyes were filled internally with lens. Thus, these small eyes were recognized as an aberration, for example a microphthalmia mutation, indicating the first record of such an aberration in A. speciosus collected in the field.