The mapping of cysts of toxic dinoflagellate in the sediment is a useful tool to determine the so called "seed bed" or "point source" where cysts are accumulated and can inoculate the water column to initiate blooms at any body of water. The first massive bloom of toxic dinoflagellate Pyrodinium bahamense var. compressum and its associated paralytic shellfish poisoning (PSP) was recorded in 1988 in Manila Bay. Progressively, it has become an annual recurrent event since 1990 in the Bay. Sediment samplings were conducted during two monsoon seasons (i.e., southwest monsoon on July-August 1993 and tradewinds on April 1996) to know the geographical distribution and concentration of P. bahamense cysts in the surface sediment of Manila Bay. Likewise, the grain size distribution of surface sediment is correlated with the accumulation and distribution of P. bahamense cysts in the Bay. Results showed that P. bahamense cysts are relatively low during the SW monsoon which ranged from 0 to 127 cysts/cm3 while during the tradewinds P. bahamense cysts are relatively high which ranged from 38 to 420 cysts/cm3. The geographical distribution of the cysts showed that the highest concentrations of 127 and 420 cysts/cm3 were constantly found in the western part of the Bay (in Limay, Bataan) during the SW monsoon and tradewinds, respectively. The eastern part of the Bay (off Manila South Harbor) also showed fairly high concentrations of the cysts that yielded 101 and 255 cysts/cm3 during the SW monsoon and tradewinds, respectively. These areas are also noted with relatively high mud silt contents of <22 mm size fine fraction. Most area of the Bay is characterized with high contents of <22 mm size fine fraction ranging from 45.5% to 90.5%, being relatively fine towards the interior and became coarser towards the mouth of the Bay. The abundance of cysts showed a clear pattern with the grain size distribution in the sediments particularly for fine fraction of <22 mm size that are accumulated in the western and eastern parts of the Bay. The western part of the Bay has been noted as the frequent origin of toxic red tide bloom in the Bay.