Background: To investigate the str uctur al diver sity of the planktonic phytoplankton thr ough summer 2009 and summer 2010, to identify the role of the main abiotic factors that determine the phytoplankton community structure and functioning and to study the summer spatial distribution of phytoplankton in relation to its potential predators such as ciliate and zooplankton. Methods: Phytoplankton and ciliate samples wer e analysed under an inver ted micr oscope after 24 to 48 h settling using the Utermöhl method. Zooplankton enumeration was performed under a vertically mounted deepfocus dissecting microscope. Results: Our r esults demonstr ated a str iking differ ence among year s is seen in suspended matter concentrations with lower values in summer 2010 (47.37 ± 23.12 mg l-1), contrasting with the higher suspended matter values in summer 2009 (92.88 ± 7.15 mg l-1). A total of 50 phytoplankton taxa identified during this study of three different algal classes (cyanobacteriae, diatoms and dinoflagellate). We found: first, in summer 2010, the phytoplankton abundance was about 3 times that in summer 2009, second, a high abundance of cyanobacteriae (43 % of total phytoplankton) and diatoms (54 % of total phytoplankton) in summer 2009 and 2010 respectively. In summer 2009, we observed a cyanobacteriae growth with dominant opportunistic and nitrogen-fixing Oscilatoria sp. Dominance of the benthic and large diatoms genus such as Navicula and Nitzschia has been reported in summer 2010. Concerning dinoflagellates, they were strongly dominated by mixotrophic and heterotrophic dinoflagellates species, like Polykrikos kofoidii, Ceratium lineatum, Protoperidinium steinii. Conclusions: This study indicates that the abiotic factor s of the coast ar ea ar ound Kneiss Islands ar e associated with the spatial and inter-annual variations of the phytoplankton. 1.INTRODUCTION The coast of Sfax is a part of the southwestern Mediterranean sea and is located in southeast of Tunisia (Rekik et al., 2012, 2016). It is bounded by the Kneiss islands in the southeast, which is composed of four little islands with Bessila is the main island, Hajer island in the north, Laboua island in the centre and Gharbia island in the south (Gueddari and Oueslati 2002). These islands are uninhabited by human populations (Mosbahi et al., 2015). The Kneiss Islands represent the most important coastal wetlands in Mediterranean Sea, and make up a very important intertidal area exploited for clam harvesting by the local population (Mosbahi et al., 2016a). The