Matabungkay and Talim Bays are two adjacent bays whose boundary is the seaward-protruding ridge, Talim Point. Both bays, facing the South China Sea, have marginal fringing coral reefs with shallow back reef portions. Several factors differentiate the two bays: energy, topography of terrains near the embaying coast, siltation rate, substrate and bathymetry. Previous sedimentological studies indicate that clay- and silt-sized sediments accumulate in Talim Bay, whereas, sand- and pebble-sized grains are higher in Talim Point zone and Matabungkay Bay. Geochemical studies also show higher relative concentrations of Ca, Mg, Sr, and Na, lower in Fe, Cu, Zn and Mn in the sediments of Talim Point zone; intermediate in Matabungkay Bay; and lower for Ca, Mg, Sr and Na, higher in Fe, Cu, Zn and Mn in Talim Bay. Five foraminiferal assemblages, defined by TWINSPAN (Two-Way Indicator Species Analysis), include: (I) Inner Talim Point zone, (2) Outer Talim Point zone, (3) Inner Matabungkay-Talim Bay portion, (4) Central Matabungkay Bay, and (5) Deeper Talim Bay assemblages. The high-energy Talim Point zone is dominated by thick-walled foraminifers which constitute a low diversity assemblage, while the low-energy Matabungkay and Talim Bays are dominated by foraminifers with thin walls which make up a highly diverse assemblage. The highly turbulent condition becomes a major controlling factor in the Talim Point zone, as only robust forms commonly occur, such as: Amphistegina, Calcarina and Alveolinella. The foraminiferal abundance in the low-energy bay portion is higher compared to the high-energy Talim Point zone. Planktonic forms are consistently few but they occur relatively higher in the outer deeper portions of the study area.