AbstractSeagrass habitats provide a range of goods and benefits to coastal communities by supporting ecosystem functioning, food provisioning, and cultural values. However, they are at risk worldwide from anthropogenic activities, climate change impacts and limited resources, which hamper efforts to protect them. Effective conservation planning requires prioritisation of sites based on multiple factors, including their relative value and vulnerability (VU). The current study examines the efficacy of combining two well-established approaches – ecosystem service assessments and habitat VU analyses – to test a method for determining conservation priority for selected seagrass meadows in Southeast Asia. Seven seagrass meadows around Southeast Asia were selected and scored by the authors based on (1) the cumulative contribution of 12 ecosystem services (ES) and the condition of the meadows, (2) VU from 16 anthropogenic threats, which were each ranked against five factors (spatial scale, frequency, functional impact, resistance and recovery time) and (3) the combination of the two approaches to create a single numerical index. Prioritisation of sites differed when meadows were scored solely for the ES they provide, compared to how vulnerable they are to anthropogenic threats. The new combined analysis brought the two metrics together to give conservation priority to sites where management intervention will yield maximum conservation benefits from conservation effort, and resulted in the prioritisation of three sites: Barrang Lompo (Indonesia), Cape Bolinao (Philippines) and Beting Tanjung Kupang (Malaysia). This method is easy to use and does not require great technical expertise. It is also auditable, allowing for clear and transparent understanding of decision-making process.