A 122 cm-long core was taken in the El-Guettiate Sebkha of Skhira (southeastern part of Tunisia) in order to investigate the recent palaeoenvironmental evolution of this region. The quantitative and qualitative analysis of ostracod and benthic foraminifera assemblages coupled with a correspondence analysis allows the reconstruction of palaeoenvironmental changes during the Holocene in this area. Four typical associations of ostracods (open marine, coastal marine, lagoonal and estuarine brackish) and two associations of benthic foraminifera (coastal and lagoonal) were distinguished. The onset of restricted lagoonal environments linked to the building-up of sand spit led to the onset of restricted lagoon and brackish environment at cal. 5408 years BP. The Shannon and equitability index of diversity were used to decipher the structural variations of the populations of ostracods and benthic foraminifera along the sampled core. We note a reduction in the Shannon index from the bottom to the top, which indicates a progressive isolation of the biotope. The open lagoonal episode is characterized by high values of diversity. During restricted lagoonal episodes the Shannon and equitability index are reduced. The correspondence analysis reveals an environmental gradient related to the marine influence. It shows an antagonism between the widely opened estuarian lagoonal species and those of restricted lagoon. The less opened estuarian lagoonal taxa occupy an intermediate position. Based on these evidences, microfauna carried out in the El-Guettiate Sebkha allows us to recognize four phases beginning with a widely opened estuarian lagoon (ca. cal. 7460 years PB), followed by a restricted lagoon (ca. cal. 5408 years BP) and finally a brackish lagoon evolving towards the present-day sebkha environment. The opened estuarine lagoon is characterized by high values of species richness and diversity indices.