Climate change is affecting the hydrodynamics of the world’s oceans. How these changes will influence the productivity, distribution and abundance of phytoplankton communities is an urgent research question. Here we provide a unique high-resolution mesoscale description of the phytoplankton community composition in relation to vertical mixing conditions and other key physicochemical parameters along a meridional section of the Northeast Atlantic Ocean. Phytoplankton, assessed by a combination of flow cytometry and pigment fingerprinting (HPLC-CHEMTAX), and physicochemical data were collected from the top 250 m water column during the spring of 2011 and summer of 2009. Multivariate analysis identified water column stratification (based on 100 m depth-integrated Brunt-Väisälä frequency N2) as one of the key drivers for the distribution and separation of different phytoplankton taxa and size classes. Our results demonstrate that increased stratification (i) broadened the geographic range of Prochlorococcus as oligotrophic areas expanded northward, (ii) increased the contribution of picoeukaryotic phytoplankton to total autotrophic organic carbon (