Diversity and structure of ciliate communities in the Gulf of Gabes (Tunisia) were investigated based on a survey of 15 nearshore stations along 237 Km, by monthly sampling over a 1-year. Ciliated protozoa were identiﬁed to genus and/or species level and enumerated. Statistic tools were used to explain the ciliates assemblage. High ciliates species richness from 133 taxa was recorded, including new records of 76 species. This study showed a longitudinal distribution of ciliate communities, which are organized in northern stations (from Tabia to Harbor of Gabes) and southern stations (from Zarrat to Jabiat Haj Ali). The number of taxa increased significantly in northern stations but decreased in the southern. This distribution was mainly influenced by the salinity and phytoplankton abundance. Ciliate taxa were grouped into fives size-classes: 15-30 µm, 30-50 µm, 50-100 µm, 100-200 µm and >200 µm. In terms of abundance, most abundant size groups were small ciliates (15-30 μm) accounted from 15 to 79 %, while the greatest biomass contribution came from the 50-100 μm size classes. We thus conclude high diversity of ciliates communities that showed a geographical distribution influenced by abiotic and biotic factors along the coast of Gulf of Gabes.