Sandwiched between the Adriatic Carbonate Platform and the Dinaride Ophiolite Zone, the Bosnian Flysch forms a c. 3000 m thick, intensely folded stack of Upper Jurassic to Cretaceous mixed carbonate and siliciclastic sediments in the Dinarides. New petrographic, heavy mineral, zircon U/Pb and fission-track data as well as biostratigraphic evidence allow us to reconstruct the palaeogeology of the source areas of the Bosnian Flysch basin in late Mesozoic times. Middle Jurassic intraoceanic subduction of the Neotethys was shortly followed by exhumation of the overriding oceanic plate. Trench sedimentation was controlled by a dual sediment supply from the sub-ophiolitic high-grade metamorphic soles and from the distal continental margin of the Adriatic plate. Following obduction onto Adria, from the Jurassic–Cretaceous transition onwards a vast clastic wedge (Vranduk Formation) was developed in front of the leading edge, fed by continental basement units of Adria that experienced Early Cretaceous synsedimentary cooling, by the overlying ophiolitic thrust sheets and by redeposited elements of coeval Urgonian facies reefs grown on the thrust wedge complex. Following mid-Cretaceous deformation and thermal overprint of the Vranduk Formation, the depozone migrated further towards SW and received increasing amounts of redeposited carbonate detritus released from the Adriatic Carbonate Platform margin (Ugar Formation). Subordinate siliciclastic source components indicate changing source rocks on the upper plate, with ophiolites becoming subordinate. The zone of the continental basement previously affected by the Late Jurassic–Early Cretaceous thermal imprint has been removed; instead, the basement mostly supplied detritus with a wide range of pre-Jurassic cooling ages. However, a c. 80 Ma, largely synsedimentary cooling event is also recorded by the Ugar Formation, that contrasts the predominantly Early Cretaceous cooling of the Adriatic basement and suggests, at least locally, a fast exhumation.