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The presence of microbial crusts (microbialites) is reported here for the first time from a Middle Miocene (Badenian) coral reef in Hungary. The succession of initiation and development of the microbial crusts is described in relation to the reef architecture. The main features of the palaeoenvironment are discussed, with focus on the associated invertebrate faunas, mostly corals, molluscs, bryozoans, and crabs. We conclude that the microbial crusts developed under normal marine conditions and were a significant contributor to reef framework development, including its strengthening through calcification of the microbial organisms. Microbialites are anticipated in other Early and Middle Miocene coral reef occurrences of the Mediterranean–Paratethys realm, and to date may have simply escaped positive recognition.