We studied the seasonal distribution of the ciliate community coupled with environmental factors along the coast at three stations sampled (from March 2006 to February 2007) in the Gulf of Gabes (Tunisia, Eastern Mediterranean Sea). A total of 56 species belonging to 11 orders, were identified. Harbor of Gabes station was more diversified (45 species) than both Tabia (26 species) and Karboub (31 species) stations. The ciliate assemblage was numerically dominated by Spirotrichea in Tabia (82% of the total abundance), in the Harbor of Gabes (86% of the total abundance), whereas, in Karboub, Spirotrichea represented only 40% of the total abundance. The unexpected lower quantitative importance of Spirotrichea in Karboub station was apparently the result of the high salt concentration found in water samples throughout the study, probably originating from the saline area surrounding Karboub station, known as Sabkha. The distribution of species in the nearshore of the Gulf of Gabes seemed most likely influenced by the combined effects of temperature, salinity and hydrographic conditions.