Two methods for separating dinoflagellate cysts from marine sediments were compared: panning and sodium polytungstate (SPT). After pretreatment with the SPT solution, Protoperidinium species had a high germination rate and cell growth rate. The germinated cells grew continuously, even in a low nutrient environment. Alexandrium cysts did not germinate, because their germination is usually active in winter. Using SPT solution, the separation process was easier, quicker, and caused much less eye fatigue than the panning method. Therefore, SPT solution offers a convenient way of pretreating dinoflagellate cysts for separation and analysis.