The present study aimed to document dinocyst ecological preferences in Ambon Bay, Eastern Indonesia, and to investigate if the bay sediments serve as a seedbank for toxic bloom events. To this end, dinocyst and geochemical analyses of surface sediment samples were performed, along with physicochemical water column parameters. Twentythree dinocyst species were identified, and high dinocyst concentrations (up to ~12,000 cysts g-1 dry sediment) were found in the inner bay. Environmental factors such as surface water temperature and salinity generally played an important role in dinocyst distribution. The concentration of Polysphaeridium zoharyi cysts showed a strong positive correlation with phosphorus. A statistically significant correlation was also found with the concentration of other autotrophic dinocysts in the sediments, and an inverse correlation was observed with the sediment C/N ratio. Cysts may serve as seedbanks for Pyrodinium bahamense blooms in the area.