Five types of reefs are described from the northern and southern parts of the Azrou-Khenifra Basin generated by the interactions of microbes and coral communities. The type 1 microbial reefs grew in both shallow- and deep-water settings, with a strong control by glacioeustasy. Type 2 microbial reefs developed in more tranquil periods, associated with common intermounds, and where only a single major regressive-transgressive sequence is recognised. Type 3 microbial reefs developed in constant deeper water conditions, generated by higher rates of subsidence in the basin, and creating an overall deepening-upward sequence. Type 4 microbial reefs recognised in the northern part of the basin have no clear counterparts in southern outcrops, but they are likely the capping strata observed in the latter area. Rugose corals allow to define a Type 5 reef, unrelated to microbial facies, and are recorded in oolitic-bioclastic backshoals or quiet inner platform settings. The presence of similar reefs in both the northern and southern parts of the basin demonstrates that conditions were not as different as previously proposed, and a lithostratigraphical, environmental uniformity occurs, which permits the analysis of different subsidence rates and glacioeustastic influence. In the Azrou-Khenifra Basin, the reefs, as well as other regional features, suggest that the basin, overall, evolved from an extensional tectonic regime during the early Brigantian into a complex extensional or compressional regime during the early Serpukhovian, passing into a predominantly compressional phase during the late Serpukhovian in a polyphase tectonic inversion during the onset of the Variscan Orogeny in the region.