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Marginal-marine to non-marine ostracod assemblages from the Bajocian (Mid-Jurassic) of southern Tunisia, precisely from the Krachoua Formation at the Kef El Anneba section near the Beni Kheddache area, are here described and tested for their utility to improve the stratigraphic accuracy and palaeoenvironmental reconstructions. This particular microfauna consists of 11 species belonging to 6 genera and represents 2 distinct types of species-rich assemblages from this time interval, allowing the interpretation of the depositional setting of the fossiliferous horizon from which the samples derive. The first ostracod assemblage is mainly composed of the brackish to shallow marine species Fastigatocythere sp. Mette, 1995; Vernoniella aff. V. bajociana Bate, 1965b; Paracypris sp. A, Paracypris sp. B, Fabanella sarda Malz et al., 1985; Marslatourella aff. M. bathonica Andreu, 1999; and Fabanella aff. F. bathonica Oertli, 1957. This ostracod biofacies reflects marginal marine (shallow platform, restricted lagoon) conditions in the studied area. In contrast, the second ostracod assemblage is exclusively dominated by the non-marine limnic species Alicenula sp., Theriosynoecum pusilla Rohr, 1976; Theriosynoecum aff. T. aveyronensis Rohr, 1976; and Theriosynoecum sp. Such ostracod biofacies reflects the establishment of (a) permanent freshwater lake(s) in the studied area, triggered by the total emersion of the Bajocian Krachoua platform, presumably as response to the short-term sea-level fall event JBj3 of Haq (2017). The recognized ostracod species from the upper part of the Krachoua Formation at Kef El Anneba section (Medenine area) are particularly similar to those already described from the neighbouring sections of Kezzani (Dhaher area) and Krachoua (Tataouine area), facilitating a stratigraphic calibration of the Krachoua Formation, as well as regional correlations of the respective Bajocian continental event within the southern Tunisian palaeogeographic domain. Moreover, the biogeography of the studied ostracod microfauna from the Mid-Jurassic of southern Tunisia provides further arguments to support the hypothesis of significant biological exchanges between Laurasian and Gondwanan islands, as recently demonstrated by means of a charophyte microflora, indicating that Peri-Tethyan biogeography remained relatively uniform during that time interval and challenging the previous assumption of their endemism.