We reported previously that okadaic acid (OA) and dinophysistoxin-1 (DTX1) were responsible for diarrhetic shellfish poisoning (DSP) incidents due to consuming cultivated mussels (Mytilus galloprovincialis) in coastal cities near the East China Sea in May 2011. Pectenotoxin-2 (PTX2) and its seco acids were also present in these mussels. Causative species of microalgae were not identified because detailed information on the location of the contaminated shellfish was not recorded. In order to explore potential causes for these poisoning events, the lipophilic toxin profiles in picked cells of Dinophysis and in shellfish samples collected from two mariculture zones in the East China Sea were analyzed in the present study. Single-cell isolates (100 cells total for each location) of Dinophysis were collected from the aquaculture zones of Gouqi Island (Ningbo City, Zhejiang Province) and Qingchuan Bay (Ningde City, Fujian Province) in July and September 2013, respectively, for lipophilic toxin profiling. Shellfish samples collected over the course of a year from the Gouqi Island aquaculture zone and mussels (M. galloprovincialis) collected four times from the Qingchuan Bay aquaculture zone were tested for lipophilic toxins by LC-MS/MS. The Dinophysis cells isolated from both sampling sites were identified under the light microscope as Dinophysis caudata. Average quota of PTX2, the predominant toxin in D. caudata isolated from the coastal waters of Gouqi Island and Qingchuan Bay, was 0.58 and 2.8 pg/cell, respectively. Only trace amounts of OA and DTX1 were detected in D. caudata. PTX2, PTX2sa, 7-epi-PTX2sa, OA, and/or DTX1 were found in samples of mussels (M. galloprovincialis and Mytilus coruscus) collected in the Gouqi Island aquaculture zone from the end of May to the beginning of July 2013. PTX2, PTX2sa, and 7-epi-PTX2sa were also detected in oyster (Crassostrea gigas) during that period, but almost no OA and DTX1 were present. Gymnodimine (GYM) was detected in almost all mussel (M. coruscus) samples, with the highest levels occurring in winter. Trace amounts of pectenotoxins (PTXs) and OAs were also found in mussels (M. galloprovincialis) collected from Qingchuan Bay. D. caudata is suggested as an important source of PTXs in shellfish cultivated in the East China Sea. This is the first report of toxin profiles for single-cell isolates of Dinophysis in the East China Sea.