Changes in the planktonic cyanobacteria structure, composition and diversity were followed over three consecutive years (2005–2006–2007) in the Gulf of Gabes (Eastern Mediterranean Sea, Tunisia). Cyanobacteria abundances, biomasses and cell lengths were measured together with selected environmental variables (pH, salinity, temperature and nutrients). The space and time variations of the cyanobacteria in relation to the environmental factors showed a close relationship between these plankton communities and the hydrographic structure of the water column. Cyanobacteria developed over semi-mixed conditions (May–June 2006) and during the thermal stratification (July 2005). The cyanobacterial abundance and biomass was evident between 20 and 35 m in inshore stations and between 20 and 25 m in deeper stations during the semi-mixing conditions and stratification. This thermocline level coincided with the euphotic layer (21.85 ± 3.76 m) allowing access of light radiation. The cyanobacteria bloom occurred during May–June 2006 when the N/P ratio (<10) was clearly below the accepted standard molar ratio of N/P = 16/1. Commonalities among cyanobacterial genera include being highly competitive for low concentrations of inorganic P (DIP) and the ability to acquire organic P compounds. Our study showed that both diazotrophic (N2-fixing) cyanobacteria such as Anabaena sp., Chroococcus sp., Trichodesmium erythraeum, Spirulina sp. and Spirulina subsalsa and non-diazotrophic cyanobacteria such as Pseudoanabaena sp. and Microcystis display a great flexibility in the N sources which allow formation of blooms.