To date, theories of eco—compensation and biological restoration have been popular, and some models in developed countries are treated as good examples. Here, we not only focus on Japan, but also pay more attention to challenges during this process. Based on a long—term field study on Sado Island, a less developed region in Japan, we attempt to describe how the government carries out environmental remediation towards the reintroduction of ibis (Species name) into the wild, and the conflict between ibis habitat restoration and farm management. We discuss the underlying reasons for this conflict and the negative effect on regional development. We follow policy improvements of the local government and related supplementary help carried out to fix the mismatch between the payment for ecological benefits and that lost by farmers in the pre—period. We conclude that the coordination of interest among different social groups is the key for success in ecological restoration and compensatory measures have to be made to meet the actual needs of the local groups. This case study in Japan can be applied to similar regions with poor environments and urgent environment restoration needs in China.