A survey of dinoflagellate resting cysts in surface sediment samples was carried out in Tokyo Bay, Japan, to document their horizontal distribution. At least 21 different cyst types were found. Dominant cyst types allowed the recognition of assemblages which form three different dinoflagellate cyst communities: the innermost part of the Bay, the central area and the mouth area. In all stations in Tokyo Bay, heterotrophic dinoflagellate cysts always occupied more than half of the cyst populations. Cysts of Polykrikos schwartzii/kofoidii are the most abundant heterotrophic species. These assemblages may reflect highly nutrient-enriched (hypertrophic) and turbulent water conditions. Among the cyst types found were probable ellipsoidal cysts of Alexandrium tamarense. This is the first record of toxic Alexandrium species cysts in Tokyo Bay sediments.