The Bajocian–Bathonian transition has been identified for the first time in the Skoura syncline of the folded Middle Atlas of Morocco based on dinoflagellate cyst and palynofacies analysis of the Ich Timellaline/Bou Akrabene Formation carbonates. This palynological study involved 109 samples of marls and limestones whose organic content yielded diverse and well-preserved dinoflagellate cyst assemblages comprising 68 taxa including stratigraphic marker taxa. Two association biozones have been defined for the late Bajocian–early Bathonian interval. The Cribroperidinium crispum-Ctenidodinium cornigerum (CC/CC) biozone is defined between the base of the Recifa Formation (Upper Bajocian) and the Ich-Timellaline / Bou Akrabene Formation (Upper Bajocian–Lower Bathonian). The second association biozone of Ctenidodinium combazii and Dichadogonyaulax sellwoodii (CC/DS) corresponds to the upper interval of the FD section (top of the Ich-Timellaline / Bou Akrabene Formation and the base of the El Mers I Formation). These two biozones were correlated with the late Bajocian–early Bathonian biozones defined in the Sub-Boreal (northwest Europe), Tethyan, and Australian domains. Close similarity between the Moroccan Middle Atlas, the Tethyan, and the Sub-Boreal domain associations has been noted. Quantitative analysis of organic matter constituents has allowed the paleoenvironmental reconstruction of the late Bajocian–early Bathonian. The organic residues of the studied samples recorded an increased land-derived phytoclasts dominance compared to amorphous organic matter and palynomorphs, indicating a proximal oxic shelf depositional environment with high terrestrial and freshwater influx during the late Bajocian–early Bathonian. During the Late Bajocian, the depositional environment corresponds to a proximal continental shelf with fluctuations from a distal to a marginal/stagnant environment.Below the Upper Bajocian–Lower Bathonian boundary, a significant marine incursion, or rather a transgression, is recorded in the studied sediments attested by an important marine fraction and dinoflagellate cysts abundance, which probably corresponds to the last Bajocian Maximum flooding surface (MFS).During the early Bathonian, the depositional environment evolved towards a distal continental shelf with an increasing marine fraction including dinoflagellate cysts and high species diversity. This may be related to the rising sea level which corresponds to the first Bathonian eustatic elevation. The proximal /marginal conditions are restored at the uppermost part of the section.