Questions: Deer-proof fencing is an essential conservation tool to protect and recover plant species diversity in deer-overbrowsed ecosystems, including species-rich sub-alpine grasslands. However, community-level conservation tools (such as fencing) may be insufficient for single-species conservation, particularly for non-target endangered or rare species that are sparsely distributed. We examined whether fencing that can protect and recover total plant species richness also benefits nontarget endangered or rare species. Location: A sub-alpine semi-natural Kirigamine grassland in Nagano Prefecture, Japan. Methods: We conducted two complementary plant surveys (typical vegetation survey using 1-m 2 sampling units and flowering survey using 150-m 2 sampling units) to account for scarce species. We examined the community-level responses (species richness, flowering species richness, and flowering abundance) of all species and endangered or rare species and the species-level responses (occurrence and flowering abundance) of each species to deer fences. Results: Fencing benefited not only the community-level response of all species, but also that of endangered or rare species. As species-level responses, about half of 43 endangered or rare species had greater flowering abundance inside the fences than outside, but only three of them showed a positive effect on their occurrence. These results suggest that once an endangered or rare species has disappeared, it may be difficult to recover. Conclusions: Continued placement of deer fences is necessary to protect community-level plant species richness of sub-alpine endangered and rare species in deeroverbrowsed ecosystems. We also highlight the necessity of additional strategies focusing on non-target individual species across broad areas outside fences.