We describe the tooth of a fossil beaver (Castoridae, Rodentia) discovered in the lower Miocene Koura Formation of Shimane Prefecture, western Japan. The specimen is an isolated, unworn left lower third molar that can be assigned to a large castorid, Youngofiber. To determine the taxonomic classification based on the internal enamel patterns of the tooth, we reconstructed those patterns using a three-dimensional image by X-ray peripheral quantitative computed tomography (pQCT). The obtained enamel patterns indicate that the M₃ of Youngofiber is characterized by a transversely elongated proparafossettid and simple synclinids running obliquely and parallel. Moreover, the present specimen retains a well developed mesostriid extending up to half the lingual height of the crown. This characteristic is shared with another castorid specimen from the lower Miocene Nojima Group in Nagasaki Prefecture, suggesting a close relationship between Koura and Nojima beavers.