On the southeastern Tunisian coastline, very diverse living microbial mats colonize the lower supratidal and intertidal zones, and locally may extend into the upper infratidal zone. The interaction between the benthic cyanobacteria and their siliciclastic substratum leads to the development of several types of microbially induced sedimentary structures (MISS). The mapping of the microbial mats has allowed the identification of the types of MISS that characterize the different segments of the coastal environment. The modern microbial mats have been compared with those recorded at the top of the Holocene deposits, which are composed of biodegraded microbial black mats alternating with white laminae made of clastic and evaporitic sediments, indicative of very high frequency cycles of flood and drought. A hypothetic profile showing their occurrences along the different areas bordering the coastline is proposed as a guide for the reconstruction of the ancient depositional environment. The roles of tidal dynamics, storms, and climate in controlling their genesis and spatial distribution, are discussed and highlighted. The modern MISS of southeastern Tunisia are compared with their equivalents that are well documented through the different geological eras.