Background : All human land use (LU) affects the distribution of plant species; however, the impacts vary with the type/intensity of LU. For managing ecosystems, it is therefore essential to understand the effects of LU types on the distribution of plant species on a macroscale. Aims : The objectives of our study were to quantify the effects of various LU types on the distribution of vascular plant species in Japan and to determine in particular the extent to which LU was an important factor for the distribution of common species. Methods : Based on a logistic regression model and variation partitioning being applied to each plant species, we evaluated the partial deviance by six LU types, four climatic types and three topographic and geological factors for 647 plant species at 14,412 sites in Japan. Results : The effect of LU was significant for species present at multiple sites. Of the six LU types, secondary vegetation and plantation were the most important factors determining species distribution for many species. Conclusions : Our results suggest that distribution of the common species is largely affected by LU on macroscale. The design of LU relating to secondary vegetation and plantations will thus be important in determining changes in the vegetation composition within Japan.