Résumé: We investigated at the single cell level during 16months (June 2012 to September 2013) the temporal distribution of picophytoplankton (picoeukaryotes, Synechococcus and Prochlorococcus) communities in two contrasted ecosystems: the Bay of Bizerte characterised by an oligotrophic regime typical of the Mediterranean Sea and the Bizerte Lagoon that exhibits a mesotrophic/eutrophic state. We aimed at depicting seasonal variations and quantifying the relationships between the environmental factors and the structure and abundance of picophytoplankton communities. Results showed that picophytoplankton groups were able to grow under a wide range of environmental conditions varying seasonally, although their abundances and contributions to the total chlorophyll biomass significantly varied and showed importance in the Bay of Bizerte. Synechococcus was the most abundant group reaching 225∗103cells·cm−3 in the Bay and 278∗103cells·cm−3 in the lagoon. This group was present all over the year in both ecosystems. Structural equation model results pointed out a different configuration regarding the picophytoplankton environmental drivers. The complexity of the configuration, i.e. number of significant links within the system, decreased under enhanced eutrophication conditions. The less exposure to anthropogenic stress, i.e. in the Bay of Bizerte, highlight a larger role of nutrient and hydrological conditions on the seasonal variations of picophytoplankton, whereas a negative effect of eutrophication on picophytoplankton communities was unveiled in the Bizerte Lagoon. We stress that such influence may be exacerbated under expected scenarios of Mediterranean warming conditions and nutrient release in coastal ecosystems.