Different approaches exist for building a system of marine protected areas (MPAs), with stakeholder-based site selection at one end of the spectrum and science-based selection at the other. Although a combination of both approaches is typically adopted, the process tends to be dominated by one of them. However, for MPAs to be successful it is necessary that their design achieves a balance between both ecological conservation and socioeconomic needs. The present study aimed to assess, compare and integrate two different approaches to the planning process of MPAs in Wales (UK). A stakeholder-based approach and a science-based systematic approach were compared. Stakeholder priorities for the establishment of MPAs were identified during individual interviews with relevant stakeholders' representatives. Science-based solutions were developed using biological and socioeconomic spatial data in the decision support tool Marxan. A comparison of the outcomes generated by both approaches revealed that although the spatial configuration of the resulting MPAs differed, stakeholders performed well at including representative proportions of relevant marine habitats and species. The integration of the stakeholder driven approach with the science-based solution revealed that an integrated approach could be used as a tool to achieve conservation targets while simultaneously accounting for stakeholder's preferences, as the resulting integrated MPA solution met all conservation targets and was only slightly larger than the science-based solution alone. Results also revealed the potential utility of using stakeholders' knowledge as a proxy for identifying ecologically important areas when spatial data on conservation features are sparse.