Past land-use activity has massively altered the environment and vegetation over centuries, resulting in range contractions and expansions of species. When habitat recovery and species recolonization require a long time, the fingerprint of past land use can remain on the current distribution of species. To evaluate millennial-scale effects of land use in Japan, we explained the current ranges of 29 mammalian genera based on three types of archaeological land-use patterns (settlement, ironwork and kiln) considering potential confounding factors. The results indicate that archaeological human activity associated with ironwork and pottery production had severe negative effects on many genera of small and medium-sized mammals. Despite positive effects on some genera, the magnitudes were less than those of the negative effects. The relative importance of archaeological factors on small mammals was greater than those for medium- to-large mammals. The persistent imprint of past land-use patterns was non-negligible, explaining current mammalian diversity. Spatial ecological and archaeological information can provide meaningful insights into long-term socio-ecological processes, which are crucial for the development of sustainable societies in the Anthropocene.