Fisheries biodiversity and production in Lake Malawi has undergone major changes including the collapse of the chambo and Labeo fishery, the exploitation of the ecologically diverse but specialized mbuna fish for food and the surge in Usipa fish production. Participatory fisheries management approaches introduced to address these challenges met with limited success due to lack of incentives for local community participation; unclear decentralized structure and roles among local fisheries management authorities; lack of management plans and agreements; and limited participation of key actors like district councils and traditional authorities. To address these issues, The USAID funded Fisheries Integration of Society and Habitats project undertook a comprehensive participatory environmental threats and opportunities assessment to establish a governance baseline in order to better understand the current status of governance and participatory fisheries management systems and identify gaps for improvement. The results from these studies have informed the development of specific interventions to address fisheries biodiversity threats, governance and management challenges to achieve sustainable fisheries management. To date, specific fisheries biodiversity and management measures, including community-managed fish sanctuaries; ecosystem and rights based approach to participatory fisheries management; integrated multiple-technology catchment activities to protect key fish breeding grounds; and improved fish handling and processing techniques, such as Vessel Monitoring System (VMS) to manage commercial trawlers and reduce conflicts between artisanal and commercial fishermen are being implemented. This research project discusses the progress made to date in implementing fisheries biodiversity management and conservation measures and shares lessons on the participatory identification of fisheries biodiversity threats and governance challenges.