Rapid and profound social and environmental changes are threatening both biological diversity and traditional livelihoods in the High Atlas Mountains, Morocco. Due to the intimate links between human and non-human populations, approaches that put local communities and their ecological knowledge at the centre of conservation strategies are necessary to halter this loss. This paper presents results from the Global Diversity Foundation’s auto-ethnographic, ethnographic and ethnobotanical research on traditional ecological knowledge of cultural practices for conservation in two High Atlas rural communities. These are practices that have an impact on maintaining local biodiversity patterns as well as culture-specific traditions and livelihoods, and are contextualised in the local layered social fabric. We elucidate the links between the agro-pastoral and water management systems, customs that utilise biodiversity and local institutions and ceremonies. Alongside Morocco’s best known ICCAs, pastoral agdals, other customary management strategies that regulate access to resources are presented. The definition of ICCA is discussed to include a gradient of territories and practices in the southern Mediterranean context. Drawing from these results as well as the GDF’s multi-cultural, multi-disciplinary experience in the “High Atlas Cultural Landscapes” project, we provide recommendations to implement successful, integrative biocultural conservation strategies.