Recent reduction of semi-natural grasslands in Nagano Prefecture, central mountainous area of Japan, caused crucial threats to grassland species of plants and insects. Many of these are considered to be relics since glacial periods that had expanded from the Asian continent probably through the Korean peninsula. The semi-natural grasslands, including pasture fields and meadows, have likely been refuges for these species in the warm and humid climate of the Holocene in Japan. Fire by humans and pasturage of horses before the modern period probably played significant roles in endurance of the semi-natural grasslands. Existence of black soil, called ‘kuroboku’, indicates the locations of the past semi-natural grasslands caused by fire since the Jomon era (the early Holocene). Areas of pasture fields since the ancient age had often been embraced in with the areas of the black soil. Moreover, statistical analyses using generalized linear model (GLM) exhibited that present distribution of endangered grassland species of bumblebees (Bombus spp.) coincide with the areas of the black soil. It suggests that the historical usage of semi-natural grasslands, regardless of human subsistence changes, has provided continual habitats for the grassland species since the last glacial period.