Multidisciplinary approaches to managing seascapes are increasingly being recognized as best practice and therefore prioritized by conservation agencies. For most coastal areas the strengthening of customary marine tenure, rules and regulations should yield even greater biodiversity and livelihood benefits. Here, we present the conservation planning results from a locally-managed marine area programme initiated by the Government of Aceh, Indonesia, which aimed to empower coastal communities to sustainably and equitably manage marine resources with local government. In 2008 the government established a Marine and Fisheries Task Force to identify priority areas for marine biodiversity (through systematic conservation planning) and coastal communities (through participatory planning). In addition to the existing 264,788 ha of marine management units, systematic planning identified another 53,372 ha. However, the subsequent stakeholder participation phase, involving intensive local consultations, further expanded the locally-managed marine area network by 6,725 ha and to a total of 23 locally-managed marine areas. This combined approach had additional benefits because it generated a strong sense of local ownership. For communities it initiated a process for recognizing their customary claimed areas and resolved overlapping boundaries between neighbouring communities, thereby reducing the likelihood of future conflicts over natural resource use. For government, it provided the basis of a robust governance system, with 34 new or revised decrees being completed and an additional USD 1.6 million being allocated for implementation of locally-managed marine areas. This participatory approach should considerably increase the successful delivery of a sustainable and equitable locally-managed marine area network for Aceh, which has wide application for the South-east Asian region and beyond.