We studied the distribution of phytoplankton and ciliate communities in relation to environmental factors at 6 stations sampled between 28 and 31 July 2006 during the summer water stratification in the Gulf of Hammamet (Tunisia, eastern Mediterranean Sea). A strong thermocline was established at 30 m, and, on average, the N/P ratio was lower than the Redfield ratio (16), suggesting a potential N limitation. The inshore location was numerically dominated by dinoflagellates (55%) represented essentially by members of the genera Protoperidinium, Gymnodinium, and cryptic Scrippsiella trochoidea and on the offshore by diatoms (68%). The phytoplankton assemblage was largely dominated by the diatoms Thalassionema nitzshioides and Rhizosolenia styliformis, while the ciliate community was numerically dominated by small taxa such as Lohmanniella oviformis (6 × 102 cells l−1) and Uronema marinum (5.50 × 102 cells l−1). The total phytoplankton abundance increased from the coastal area (5.26 × 102 ± 4.48 × 102) to the open sea (10.33 ×102 ± 28.06 × 102) and decreased from the surface to the bottom, inversely to the ciliate abundance. Total phytoplankton and abundances showed similar patterns. Total ciliate biomass decreased from the inshore (0.25 ± 0.58) to the offshore (0.06 ± 0.10) areas but increased from the surface to the bottom. The diversity index of both phytoplankton and ciliate communities showed a decrease with a coastal–open sea gradient. The relationships between phytoplankton and ciliates suggest planktonic micro-heterotrophs were implicated in the channelling of matter and energy through the microbial loop in the Gulf of Hammamet.