The surface sediments off Southwestern Taiwan were collected during three different cruises in May 2009, November 2009, and March 2010, respectively. The concentrations of chlorophyll-a and phaeopigment, as well as benthic foraminifera species, were analyzed. The results show that the concentration of chlorophyll-a decreases with the distance from the shore, and the concentration of chlorophyll-a also decreases with increasing water depth. The concentration of phaeopigment seems to have no significant relationship with the water depth. The relationships between the concentrations of benthic foraminifera, chlorophyll-a, and phaeopigment are also not significant. Because samples were collected from different water depths on the continental shelf, slope and in a canyon, the oceangraphic setting therefore may be one of the main factors which influences the distribution pattern of benthic foraminifera. According to the EOF analysis, the water depth in sampling sites plays a very important role in terms of the distribution of living benthic foraminifera in this study. The distribution do not show significant difference between collecting seasons. Finally, the concentrations of the chlorophyll-a and phaeopigment decrease drastically in a downcore record. Quinqueloculina spp., an epifaunal foraminifer, shows a significant peak concentration in the depth of 5-6 cm downcore. Bioturbation probably was responsible for this change.