There is currently a significant imbalance in existing marine resource management frameworks. Across Africa and the Middle East there is a developing network of marine protected areas focused on natural heritage but with very limited engagement with area-based management for cultural heritage. Yet both natural and cultural heritage resources are subject to the same considerable threat levels from both natural and anthropogenic processes of change. The MarEA project is engaged in an extensive programme of mapping and documentation of endangered cultural heritage sites and landscapes across the MENA region. During the course of this and aligned work, its engagement with coastal communities and international practice has identified a clear need for more informed and holistic approaches to marine resource management. This study presents a model for the integrated management of natural and cultural heritage and proposes a framework for the future identification and designation of Marine Cultural Heritage in Protected Areas.