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This work proposes a regionalization of marine waters south of the Iberian Peninsula, north Morocco and Algeria based on empirical orthogonal functions and GIS analysis. The regions identified are consistent and correspond to hydrological mesoscale and macroscale structures well characterized from physical and biological viewpoints. Although it is difficult to determine the boundaries of a fluid continuously moving, the procedure used recognizes the most frequent patterns and can be used to geographically reference the most likely position of the limit among the regions. Once established the regions, the connectivity among them is addressed by means of geostrophic currents derived from altimetry data. The main geostrophic circulation pattern depict an elevated connectivity in the area that might facilitate the conservation and recovery of species, but also imply a higher vulnerability to negative external forces and highlight the need of models, marine spatial planning, and coastal management approaches that include the pelagic ecosystem and connectivity of the seas. Furthermore, the results confirm that the cooperation between public authorities at different levels (local, regional, state) as well as among coastal countries is essential for Marine Spatial Planning (MSP) and prevention of potential risk derived from upcoming marine activities in the framework of the 2020 Agenda and Blue Growth Strategy ( European Commission, 2012 ). The recently approved Directive for Marine Spatial Planning and Integrated Coastal Zone Management ( European Commission, 2013 ), with the objective to avoid conflicts among diverse users and guarantees stable environment and sustainable growth, requiring information concerning regionalization and connectivity in the sea, but this information is not always available in all regions, space and time scales. Our approach offers a cheap, fast and universal applicable methodology for mesoscale regionalization and connectivity estimation as a starting point of a nested MSP approach until further detailed oceanographic studies can be carried out at the most interesting points identified in the respective area considered in the MSP. [ABSTRACT FROM AUTHOR]