The Middle Jurassic – Early Cretaceous period witnessed the emergence of some major representatives of modern continental vertebrate groups (stem lissamphibians, squamates, therian mammals and birds) and angiosperms, at a time when fragmentation of Pangaea was underway. The successive Moroccan microvertebrate faunas of Ksar Metlili (?Berriasian) and Guelb el Ahmar (Bathonian) from the Anoual Syncline significantly improve our poor knowledge of Gondwanan and especially African palaeobiodiversity at this time. They are among the richest known from the Mesozoic of Gondwana, and are well placed in northwestern Africa to record faunal interchanges with Laurasia. Here we focus on the Ksar Metlili fauna, first documented in the 1980s and most recently resampled in 2010, which produced 24 541 microremains representing 47 species of 8 main groups (Chondrichthyes, Actinopterygii, Sarcopterygii, Lissamphibia, Lepidosauromorpha, Testudinata, Archosauromorpha and Synapsida). It includes remarkable taxa: the oldest stem boreosphenidan mammals from Gondwana, probably some of the last non-mammaliaform cynodonts, a basal ornithischian, possibly freshwater teleosaurid crocodylomorphs, and some of the rare occurrences of choristoderes and albanerpetontids in Gondwana. Comparison of the Ksar Metlili fauna with that of Guimarota (Kimmeridgian, Portugal) further provides evidence of numerous shared taxa of Laurasian affinities, in contrast to the occurrence of few taxa with Gondwanan affinities. This suggests complex palaeobiogeographical relationships – implying both vicariance and dispersal events – of North Africa within Gondwana at the Jurassic–Cretaceous transition. Finally, the faunal similarities with the Guelb el Ahmar fauna question the Cretaceous age of the Ksar Metlili fauna, suggesting an alternative possible Late Jurassic age.