Highlights: • Picophytoplankton was able to grow under a wide range of environmental conditions varying seasonally. • Picophytoplankton variability was more marked in the bay than in the lagoon. • Picophytoplankton decreased in the lagoon under enhanced anthropogenic stress. • Synechococcus, the most abundant group of the community, was frequently present in both ecosystems during the monitoring. 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 th...