As urbanization and biodiversity loss especially of rare species are coinciding and accelerating global trends. Therefore, to find potential conservation sources for rare species is becoming increasingly important in urban area. We conducted a field study to survey rare plant species in 7 land use types (park, vacant land, cemeteries, agricultural land, sports facilities, universities and natural area) of Tokyo and surrounding areas. The aim of this study was to find potential land use types as conservation sources for rare plant species in urban area. In this study, we recorded 328 vascular plant species, including 9 endangered plant species and 152 rarest plant species. We found different land use types have no big effect on average plant species number. However, mean endangered plant species richness is higher in agricultural land than park and university and mean 0.1% rarest plant species richness is higher in natural area than other land use types. Also, environment factors like urbanization level, have effect on rare plant species richness. In conclusion, this study provides evidence that some land use types in urban area are truly contribute to the conservation of rare plant species.