Recently sika deer (Cervus nippon) has been overabundant in many places of Japan, including Yakushima Island and Shiretoko Penninsula that are the World Natural Heritage.  Deer has a big impact on natural vegetations and agriculture and forestry.  In Yakushima Island, not a few endemic plants (e.g., Athyrium yakusimense) are threatened by deer (C. nippon yakushimae).  To prevent these plants from going to extinct, we considered a population management plan of deer. We divide three regions in Yakushima Island, Western-, Northeastern, and Southern regions.  (i) Western Region includes a big area of the World Heritage, a big (>5000) population of deer and its vegetation has been heavily damaged. (ii) The deer population increases in the Northeastern Region.  (iii) A relatively rich vegetation remains in the Southern Region.  If the total yield of deer does not increase in the future, we recommend hunters focusing all hanting effort on the Southern Region.  If the yield is as three times as it is, hunters are able to control the Northeastern and Southern Regions.  We discuss the risk and uncertainty in the population management model.