Thermal stratification is increasing in strength as a result of higher surface water temperature. This could influence the vertical distribution of vertically migrating dinoflagellates. We studied the diel vertical distribution of the dinoflagellates Heterocapsa triquetra and Prorocentrum minimum using stratified laboratory columns with two thermoclines of different strength (Delta TA degrees A = 10 or 17 A degrees C), with below cline temperature of 8 A degrees C. Above the thermocline, nutrient depletion simulated the natural summer conditions in the Baltic Sea. Our study shows that H. triquetra and P. minimum can behave differently in terms of their vertical occurrence, both in space and in time when subjected to thermoclines of different strength. Also, both dinoflagellate species showed species-specific distribution patterns. In the Delta TA degrees A = 10 A degrees C treatment, H. triquetra cells performed a diel vertical migration (DVM) behavior just above the thermocline, but not in the Delta TA degrees A = 17 A degrees C. In the Delta TA degrees A = 17 A degrees C, the cells did not migrate and cell densities in the water column decreased over time. Opposing results were observed for P. minimum, where a DVM pattern was found exclusively below the thermocline of Delta TA degrees A = 17 A degrees C, while in the Delta TA degrees A = 10 A degrees C treatment, no clear DVM pattern was observed, and the highest number of cells were found in the cold bottom water. These results indicate that an increase in thermal stratification can influence species-specific dinoflagellate distribution, behavior, and survival.