This paper presents a proposed methodology for the integration of ecosystem-based management and conservation of focal resources in protected areas via a prioritization process for resource conservation. The proposed methodology relies upon a prioritization of resources, determination of resource vulnerability, and integration into a spatial conservation planning tool. First, the origins and scientific basis for ecosystem-based marine management are reviewed. Next, the concept of ecosystem vulnerability as a method for integrating ecosystem and focal resource protections is proposed. A comprehensive planning process and three-step method are then described for quantifying vulnerability for use in marine spatial planning (MSP) tools. Finally, specific applications to management of protected areas are articulated.