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Marine ecosystems are increasingly threatened by multiple anthropogenic pressures, leading to biodiversity loss, habitats degradation and resources deterioration. To address these challenges, international and regional policy frameworks have established conservation targets. Ecologically or Biologically Significant Marine Areas (EBSAs), designated by the Convention on Biological Diversity based on multiple criteria, can guide spatial conservation and play a vital role in maintaining ocean health. In this study, we provide a quantitative, systematic approach to refine existing EBSAs within the Western Mediterranean Sea via spatially explicit proxies for the internationally agreed protection criteria. Spatial prioritization was conducted and included environmental stability to account for ecological resilience under climate change. Our results reveal a pronounced spatial imbalance in the representation of EBSA criteria within internationally agreed protection schemes (Natura2000 sites, Ramsar sites, Specially Protected Areas of Mediterranean Importance and proposed Sites of Community Importance), ranging from 2.2 % to 63.9 %, providing relevant information for the study area. There is a marked bias toward the northern part of the basin, with current EBSAs covering 47 % of the study area, while existing protected spatial features correspond to 19.7 % of the study area. This spatial bias may undermine the effectiveness of marine biodiversity conservation and highlights the need for more equitable and data-driven spatial planning approaches. By redefining existing EBSAs and evaluating their alignment with internationally agreed protection schemes, our work provides a scientific basis to inform future conservation strategies and support the development of ecologically coherent transnational networks of protected areas aligned with global and regional goals. • Marine ecosystems face growing threats from human activities. • EBSAs guide marine conservation using qualitative data linked to seven criteria. • Current protection shows a spatial bias, mostly favoring the north region. • This study supports ecologically coherent transnational protected area networks.