The Alboran Sea is highly dynamic from a hydrographical point of view. Depending on the strength of the currents and the direction of the wind the surface coastal water masses can be either of Atlantic or Mediterranean origin. This variability affects both the phytoplankton and zooplankton components of the community inhabiting the Bay of Málaga. In addition, fish larvae distribution varies with the diel cycle, affecting zooplankton distribution in shallow waters. In order to provide a first insight into the variability of the planktonic community composition in the area during a 24 hour cycle, we applied an integrative approach combining morphological and molecular tools.