We compared the distribution patterns of five mammals in the Jomon period (12,000– 2,400 years before present time), middle Edo period (1730s), and the present (ca. 1978–2000) using three existing databases. Cervus nippon was widely distributed from Hokkaido to Kyushu during the Jomon and Edo, but absent from most of northern Honshu in the present age. Sus scrofa was widely distributed from southern Hokkaido to the Ryukyu Islands in the Jomon, but absent from Hokkaido in the 1730s and from northern Honshu in the present age. Macaca fuscata was distributed from the northern-most region of Honshu to Kyushu in the Jomon and Edo periods, but diminished in northern Honshu and exhibits a fragmented distribution in the present age. Ursus arctos and/or U. thibetanus were distributed from Hokkaido to Kyushu in the Jomon and 1730s, but greatly diminished in Kyushu in the present age. The distribution patterns of these five mammals changed little from the Jomon to the Edo periods, but were greatly diminished between the Edo and present periods. We suggest that the distribution of mammals changed due to direct (hunting) and indirect (habitat alteration) humanmammal interactions.