As urbanization accelerates globally, natural remnants were decreased drastically, while many new land uses including university campuses were boomed in urban ecosystems. Previous studies reveal that natural habitats in urban areas can harbor rare species richness. However, a key question on the contribution of anthropogenic habitats to rare plant species remains critically open in Japan. In our study, we conducted a comprehensive assessment of rare species of natural remnant and anthropogenic habitats in urban ecosystems along the urban gradients. We evaluated the functional rarity of the 170 plant species, and the distribution of functional rarity and functionally rare plants for different urban land uses in the megacity of Tokyo. We found both natural remnants and anthropogenic habitats can be potential conservation sources to support functionally rare species in urban ecosystems. University campuses performed best in protecting functionally distinct species and scarce species in the high urbanization level area except for parks. Hence, we argue that anthropogenic habitats can be helpful in urban functionally rare species conservation, and university campuses play an important role in rare species conservation at the urban core area.