Many rural communities in the global South – including some 370 million indigenous peoples – are directly dependent on biodiversity and related traditional knowledge for their livelihoods, food security, healthcare and well-being. But with the loss of biodiversity, valuable resources such as climate-resilient crops, medicinal plants and wild foods are being lost. Cultural diversity is being eroded at an unprecedented rate and with it, ancestral knowledge of how to use and conserve biodiversity. This special issue of Participatory Learning and Action explores two important participatory tools that indigenous peoples and local communities can use to help defend their customary rights to biocultural heritage: i) Community protocols – or charters of rules and responsibilities – in which communities set out their customary rights to natural resources and land, as recognised in customary, national and international laws; and ii) Free, prior informed consent (FPIC) processes, in which communities decide whether or not to allow projects affecting their land or resources to go ahead, and on what terms. The issue reviews the experiences of communities in Asia, Latin America and Africa in developing and using these tools in a range of contexts, including: developing mechanisms for access and benefit-sharing (ABS) for genetic resources and traditional knowledge; confronting threats from mining and protected areas; and improving forestry partnerships. It also looks at government experiences of establishing institutional processes for FPIC and benefit-sharing. It identifies practical lessons and guidance based on these experiences and aims to strengthen the capacity of a range of actors to support these rights-based tools effectively in practice. This special issue aims to provide guidance for those implementing the Nagoya Protocol and other natural resource and development practitioners, and to raise awareness of the importance of community designed and controlled participatory processes.