The Permian–Triassic transition has been identified for the first time in the Karoo Supergroup of the Moatize–Minjova Basin in Mozambique. This transition was identified in the subsurface in deep (ca. 500m) coal exploration boreholes that penetrated the Matinde Formation. Two palynomorph assemblages (assemblage 1 and assemblage 2) assigned to the latest Permian were defined for the Matinde Formation. These assemblages are both dominated by taeniate pollen, cavate trilete spores of Kraeuselisporites spp., associated with conifer (Lueckisporites virkkiae) and pteridosperm pollen (Guttulapollenites hannonicus and Weylandites lucifer). Assemblage 3 represents a microfloral turnover. For the first time specimens of Lunatisporites pellucidus appear in an assemblage dominated by lycopod spore taxa such as Lundbladisporites spp. This assemblage was assigned to the Early Triassic and occurs at the top of borehole DW 132 within the Matinde Formation. The palynostratigraphic signature obtained for the Permian–Triassic transition puts the Moatize–Minjova Basin in the central Gondwana palaeobiogeographic province with strong affinities with the Karoo basins of Madagascar and the Salt Range Basin in Pakistan. These new data indicate that coal deposits accumulated in the Moatize–Minjova Basin until the latest Permian and that these are possibly more extensive temporally than previously described, opening new perspectives for coal and unconventional hydrocarbon exploration in this basin. Display omitted •Permian–Triassic transition was identified in Karoo succession in Mozambique.•Mozambique was part of the central Gondwana palaeobiogeographic province.•Data opens new perspectives for coal and unconventional hydrocarbons exploration.