Using data sets for Japan as a whole, as arranged with approximately $10{ imes}10$ km squares (a secondary grid), we investigated the relationship between population density and the habitats of threatened vascular plants listed in the Japanese Red Data Book; depopulated areas in the present and future, areas where under-use may be serious, and those with a predominance of elderly people; and the present state of the habitats in terms of a characteristic land use pattern. Regarding the habitats of threatened vascular plants, the progress of deterioration [$(N_{CR}+N_{EN})/(N_{CR}+N_{EN}+N_{VU})$] in depopulated areas has been confirmed, where $N_{CR}$, $N_{EN}$, and $N_{VU}$ are the numbers of species classified as critically endangered, endangered, and vulnerable, respectively. Moreover, in grid squares used by a human such as farmland, the progress of the deterioration simply increases when population density becomes low. However, for many vascular plants, they are particularly endangered in populous areas. Local populations will decrease throughout Japan with the rate of depopulation in and around large cities being relatively slow. We also propose some issues that need further study. The deterioration by human activity may be reduced. On the other hand, some vascular plants may be adversely influenced by depopulation. Additionally, we should keep a close watch on grasslands and water areas in large cities to preserve vascular plants.