Jayapura Regency is a strategic area in Eastern Indonesia, which is supported by natural resources in the agricultural sector and tourism potential. In managing natural resources, especially agriculture towards tourism is influenced by policies that erode the community into patterns that eliminate work culture systems, innovation systems, and low farmer knowledge. Therefore, holistic, thematic, integrative, and spatial governance is needed with an upstream initiation in the form of an independent village. This study aims to describe the concept of mechanisms and governance needed to encourage the growth of independent villages in Jayapura Regency within the limits of collaboration, involvement, and communication based on regional innovation systems. The research method uses a description of mechanisms and governance which is limited to five components, including partnerships, networks, and collaborations; Community presence and engagement; External communication strategy; Communication material; and Advocacy and policy involvement based on RIS. The study focus was carried out in Jayapura Regency with the target of independent villages in Sentani Timur District and Kemtuk Gresi District. The results show that the mechanism and governance model with the limitations of partnership, network, and collaboration; community and engagement; external communication strategy; communication material; and advocacy and policy engagement based on regional innovation systems can be implemented in independent village agrotourism. This study implies that policymakers have references to pilot projects for village-level economic development based on local potential and pilot projects for local governments in managing the concept of development from a holistic, thematic, integrative, and spatial perspective.