Here we describe a 14-year collaboration in New Ireland, Papua New Guinea, between an Indigenous NGO, Indigenous scientists and international researchers. New Ireland is a marine province in the Western Pacific region where most residents depend on fishing, marine gleaning and small-scale gardening for their livelihoods. Ailan Awareness is a locally founded and managed NGO that focuses on the strengthening of Indigenous sovereignty regarding biological, cultural and spiritual diversity as well as fostering Indigenous epistemology practices and strengthening biocultural diversity. In partnership with anthropological researchers, Ailan Awareness has designed an approach to marine conservation informed by the growing field of decolonial research practices. By working to empower coastal communities to make decisions about their marine and cultural resources using a mix of Indigenous, anthropological and scientific methods and giving primacy to strengthening Indigenous modes of knowledge production and the role of community Elders, Ailan Awareness addresses a major gap in the efforts of the national government and international NGOs: giving the people most directly affected by declining biodiversity and loss of tradition the support and tools required to design and carry out the strengthening of both biological diversity and traditional social practices. In this paper we describe the methodology used by Ailan Awareness and the history of collaboration that resulted in these methods.