The Yuigahama Chusei Shudan Bochi site (AD: twelfth to thirteenth centuries), located along the seashore of the southern end of Kamakura City in Japan, and has yielded a mass grave containing hundreds of human crania. The purpose of this study is to document cut marks on crania made by an edged weapon, paying specific attention to individuals who may exhibit scratch marks, and to understand the variability of weapon-related traumas in the medieval period in Japan. The observation leads to tentative findings regarding the identification and interpretation of weapon-related traumas of human skeletal remains. From macroscopic observation, the marks display the sharpness of cut surfaces which are characteristic of unhealed cut marks. Scanning electron microscopic observation of the marks also shows that they are V-shaped in cross-section, a morphological feature that is characteristic of cut marks. This study first demonstrates that the scratches on the crania have morphological features consistent with human-induced cut marks, and that the macroscopic and microscopic approaches provide important information for identifying anthropogenic cut marks on the human skeletal remains from an archaeological site in Japan.