Preliminary analysis of the dinoflagellate cyst assemblages in sediment cores from two sites in Manila Bay, i.e., Cavite, a toxic red tide prone area, and Pampanga, an area with less red tide outbreaks, are presented. At least ten cyst species were present at the Pampanga area, including the main toxic species Pyrodinium bahamense var. compressum. The cyst assemblage in this area was dominated by Protoperidinium spp. followed by Gonyaulax spp. Pyrodinium bahamense var. compressum was also seen in Cavite, which contained cyst species similar to the Pampanga core. However, Cavite appeared to have a higher concentration of dinoflagellate cysts than Pampanga. This difference may be related to differences in productivity, or degrees of eutrophication. However, this could also be a reflection of the diluting effect of greater amounts of sedimentation at Pampanga due to its proximity to the Pampanga River, the largest source of sediment in Manila Bay. Such differences have important implications in toxic red tide management and in choosing sites for mariculture in the Bay.