For the first detailed study on species composition and biogeographical distribution of Pseudo-nitzschia in Chinese waters, net and water plankton samples were obtained during four seasonal cruises from five representative areas along the Guangdong provincial shoreline in the South China Sea. In total, fourteen Pseudo-nitzschia species were identified morphologically: P. americana, P. brasiliana, P. caciantha, P. calliantha, P. cuspidata, P. cf. lineola, P. mannii, P. multiseries, P. mutistriata, P. pseudodelicatissima, P. pungens, P. sinica, P. subfraudulenta and P. subpacifica. Seven taxa are new records for China, two are new for Asia. Detailed morphometric data were obtained using light microscopy (LM) and transmission electron microscopy (TEM). P. subpacifica had a smaller valve width than previously described. P. cuspidata and P. cf. lineola deviated in valve width and interstria density. Species diversity and relative abundances (percentage) of Pseudo-nitzschia spp. were maximal in summer (July 2006), followed by spring (April 2007) and minimal in winter (January 2007). Pseudo-nitzschia calliantha, P. subfraudulenta, P. caciantha, P. pseudodelicatissima and P. pungens were commonly recorded in Guangdong coastal waters. Pseudo-nitzschia subfraudulenta dominated the total microphytoplankton in Daya Bay during summer and its relative abundance was 49.86%. Pseudo-nitzschia calliantha was the markedly dominant species in other three areas during summer and its relative abundance was 73.43%, 81.76% and 83.1% in Hailing Bay, Shantou Harbour and Zhelin Bay, respectively.