Bees are an important faunal group and function as pollinators for various flowering plants. The diversity and abundance of bees have decreased in some parts of the world, which has led to fears about habitat degradation and a pollination crisis worldwide. Decades ago, a group led by Shoichi F Sakagami established a systematic method of bee surveys and systematically conducted intensive bee surveys in Sapporo on the campus and Botanic Garden of Hokkaido University in 1979 and 1989. These involved sampling bees and recording the flowers that were visited by the bees from April to September. Here, we have converted this to digital data by archiving the data on the bee species and the plant species that the bees visited in 1979 and 1989 at two sites at Hokkaido University, in Sapporo, Japan.