A sediment trap study was conducted at Daya Bay, South China Sea, to investigate the relationships between encystment and population dynamics of Scrippsiella trochoidea from December 1999 to January 2001. A dense bloom of S. trochoidea occurred during the study period from August to September 2000, with the maximum cell number of 3.18 × 104 cells mL−1. Two morphotypes of cysts, one with a thick calcareous wall (calcified cyst) and another without the obvious calcareous cover (non-calcified cyst), were observed during this investigation. The morphological and excystment characteristics of these two cyst types were studied as well. Mass encystments of S. trochoidea, with the maximum of 3.05 × 105 cysts m−2 d−1 for calcified cyst, and 1.54 × 107 cysts m−2 d−1 for non-calcified cyst, coincided with the maximum abundance of the vegetative cells. Encystment caused the transfer of a total of 2.24–4.49 × 108 cells m−2 vegetative cells from the water column to the sea bottom during the bloom and resulted in a considerable loss of the bloom population. High assemblages of cysts of S. trochoidea were detected in the surface sediments as well. This rich ‘seed bed’ in the surface sediments caused by the high efficiency of encystment after blooms acting as a benthic reservoir for future vegetative population, together with the short dormant period (15–26 days) and high germination rate (50–90%), may explain the repeated occurrence of S. trochoidea blooms in Daya Bay.