Dinoflagellates underwent a major radiation during the Bajocian (Middle Jurassic, ~ 170–168 Ma). The group originated in the Middle Triassic and dinoflagellate cysts were relatively low in diversity until the Bajocian, when over 100 species appeared. The Gonyaulacaceae expanded during this interval to become the dominant family of cyst-forming dinoflagellates, and has remained the principal dinoflagellate family throughout the Mesozoic and Cenozoic. However, Bajocian dinoflagellate cysts have received relatively little study. In order to unravel the pattern of the Bajocian dinoflagellate radiation, we have generated a high resolution, quantitative, palynological record through an expanded Middle Jurassic succession in Swabia, southwest Germany. Previous research has indicated a rapid, stepwise order of first appearances through the Bajocian. By contrast, we clearly demonstrate that there was a more gradual, continuous increase in diversity from the Late Aalenian to the Early Bathonian, although the number of first appearances was highest during the latest Early Bajocian to Late Bajocian. Major experimentation in excystment mode in the gonyaulacaceans occurred during the Late Aalenian and Early Bajocian, when multi-plate precingular, single-plate precingular and epicystal archaeopyle types first appeared. Through the integration of our data with published information from northwest Europe, we demonstrate that the appearance of dinoflagellate cyst taxa through the Late Aalenian–Early Bathonian appears to have been controlled by a major second-order transgression. Although the cause of this radiation is yet to be constrained, given the contemporaneous diversifications of other plankton groups, as well as ammonites, bivalves and fishes, it is likely that it formed part of the wider Mesozoic Marine Revolution. There is a prominent acme of Dissiliodinium giganteum in the Lower Bajocian which is a useful stratigraphical marker. Acanthaulax crispa is confirmed as a key index species for the Bajocian. One new species, Korystocysta aldridgeii sp. nov., is described.