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Multi‐scale transgressive–regressive cycles from the mid‐Jurassic were recognised in the Central Lusitanian Basin, Portugal. These cycles allow the depositional evolution of the basin to be better understood and aid in the construction of stratigraphic sequences composed of three hierarchies. The stacking pattern of high‐frequency transgressive–regressive sequences forms larger clusters that define medium‐frequency transgressive–regressive sequences. Likewise, the stacking pattern of medium‐frequency transgressive–regressive sequences generates two Bathonian–early Callovian low‐frequency transgressive–regressive sequences. Integration of several methods supported the interpretation of facies associations representing clastic deposition in offshore to shoreface environments and carbonate sediments in outer to inner ramp settings. New data from calcareous nannofossils and dinoflagellate assemblages constrained the interval's Bathonian–early Callovian age, thus unveiling the Middle–Upper Jurassic disconformity and filling the Middle Jurassic stratigraphic record gap in the Central Lusitanian Basin. This study may be helpful for similar successions in Tethyan domains and comparable depositional settings elsewhere. [ABSTRACT FROM AUTHOR]