In a grid investigation, dinoflagellate cysts were collected from sediments in Xiamen Western Harbor in May of 2000,from which five species of cysts were identified: Alexandrium tamarensis, A. minutum, Lingulodinium polyedra,Gonyaulax scrippsae and Gymnodinium catenatum, account for about 21% in the species composition. The quantitative analysis of the sediments shows that the number of dinoflagellate cysts varies from 51 to 256 cysts/g of sediment, the highest value (>200 cysts/g) being recorded at the stations of the central part of the bay, while the lowest (＜100 cysts/g) at the bay mouth. A good linear relationship is found between cyst amount and fine-grained sediments. Complex physiognomies on the seabed, topographty in the bay and weak water exchange are the main factors not only in cyst accumulation but also in their distribution pattern, and have resulted in the difference in cyst densities between the inner bay and the outer bay in the harbor.