Microalgal populations along French coasts (English Channel, Bay of Biscay and Mediterranean Sea) have been sampled twice a month since 1987 within the context of the French Phytoplankton and Phycotoxin Monitoring Network (REPHY). This study used these data to characterize the large-scale geographical structures of microphytoplankton communities and to determine whether 'homogeneous' geographical areas exist in which microalgal populations display similar temporal variability schemes. Once the temporal variability component shared by all sampled coastal sites was identified, the 'residual' site-specific component was analyzed. Multivariate ordination methods were used to determine seasonal and inter-annual variability. The expected-temporal pattern common to all sites was identified and the seasonal cycle of the most frequently observed phytoplankton communities along French coasts was described. The between-site analysis, using multitable comparison methods (RV-coefficient and multidimensional scaling), allowed the identification of 3 large areas (western English Channel, Bay of Biscay and Mediterranean Sea) according to the temporal variability patterns of microphytoplankton populations. The results, despite the coastal locations of REPHY sampling sites, indicate that the hydrodynamic characteristics of the different areas play a major role in the geographical structure of microalgal populations in French coastal waters.