An exploration well drilled at the Middle Eocene fossil site of Messel, near Darmstadt, Germany proved that the famous Messel oil shale was deposited in a maar lake. During a quantitative palynological investigation of the entire succession of lake sediments, a monospecific population of dinoflagellate cysts was encountered. Based on transmitted light and scanning electron microscope (SEM) studies, they are assigned to the new peridinioid taxon Messelodinium thielepfeifferae gen. et sp. nov. because they are acavate and lack distinct apical or antapical horns. The dinoflagellate cysts exhibit considerable intraspecific variation in surface ornamentation. Messelodinium thielepfeifferae gen. et sp. nov. is abundant in sediments of the early holomictic stage of Lake Messel, but generally is reduced in frequency in the oil shale which represents the meromictic stage. These dinoflagellate cysts appear in peak abundances in mass flow and debris flow deposits in which material from the lake shore was transported downslope to the basin center. Thus, major concentrations of Messelodinium thielepfeifferae gen. et sp. nov. occurred in nearshore environments either due to primary population density of the parent motile stage, or due to secondary cyst accumulation by wind and wave action. The dinoflagellate cysts are notably absent in the uppermost 25 m of the core, where Botryococcus dominates. This shift in algal populations is interpreted as a response to changes in the chemistry of the water body.