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A bloom of the dinoflagellate Scrippsiella trochoidea was detected for the first time in inner Tolo Harbor, Hong Kong in 2000. Water samples were collected at eight stations along a transect passing through a red tide patch for microscopic analysis of phytoplankton composition and high-performance liquid chromatography (HPLC) analysis of phytoplankton pigments. During the bloom, the density of dinoflagellates was 1.1×106 cells L-1 within the patch and 8.6×105 cells L-1 outside the patch where the phyto-plankton community was dominated by diatoms. After the bloom the S. trochoidea began to decrease in density and was replaced by diatoms as the dominating bloom-causing organisms at all stations, and the density of dinoflagellates at most stations was less than 1.0×106 cells L-1. The status of S. trochoidea as the causative species of the bloom was indicated by the presence of peridinin, the marker pigment for dinoflagellates. The shift from dinoflagellates to diatoms was marked by the decline of peridinin and the preva-lence of fucoxanthin. Phytoplankton pigment markers also revealed the presence of other minor phytoplankton assemblages such as cryptomonads and blue-green algal.