The present article reported the processes and key issues that arose during the development of the self-governance framework for hunting activity in Cilamitay, an Amis community in Fuli Township, Hualien County. The major developments of constructing this framework included the designation of a hunting management area, the integration of a traditional age-hierarchy system (the sakaputay), and the establishment of a multi-organization decision-making platform. By incorporating groups from various backgrounds, namely local ndigenous cultural and new groups, government agencies and academic representatives, the process not only promoted Amis identity, but also successfully bridged local knowledge, scientific knowledge and present administration regulations. It was decided that the self-governing hunting organization should be established with the traditional tribal leaders (the yakuing; also known as tribal council) appointed as the board of directors and the ciputay (the managerial level of the sakaputay) assigned as the executive body, so both respective groups can directly contribute to this new organization. Other residents, which include existing local groups, regional representatives, and Han Chinese will also be invited to participate. In the present study it was found that: (1) the indigenous community and local governments are key parties during the framework establishing process, and their respective roles and responsibilities will require continual evaluation throughout the whole process; (2) integrating various local groups is essential to avoid bias; (3) communication and trust-building between the two parties can be greatly improved by the involvement of a trustworthy third party (e.g., experts or non-governmental organizations); (4) communication between the different parties during the process should take into account the tribal culture, while adhering to the present legal system, social expectations and ecological knowledge; (5) due to the uncertain outcome of the validation of the Indigenous Traditional Territory, it is recommended that a community should start its management of hunting activity in an area that does not overlap with the hunting activities of other indigenous communities; (6) the transfer of governance authority to the proper local organization will enable effective management practices applied to the designated area. Lastly, because the establishment of the self-governance organization for hunting is an ongoing process of negotiations, as well as mutual understanding among different knowledge systems (i.e., traditional knowledge vs. scientific knowledge), which can be difficult to replicate, it is recommended that each community should stablish their organizations adhering to their own customs and contexts for increased effectiveness. The experience learned from the Cilamitay project, as case study, should be helpful in reducing communication barriers and conceptual gaps between indigenous communities and the government.