Rapid proliferation of toxic or noxious microalgae in the sea, which is termed as harmful algal bloom (HAB), can lead to serious impacts, such as fish kill, seafood contamination, tourism impairment and ecosystem degradation. Blooms of toxic algae are considered as a major group of HABs, leading to public health impacts due to the production of toxins. Toxic algal blooms receive increasing concern in China. Most of the toxic algal blooms in the coastal waters of China were caused by Alexandrium spp. producing paralytic shellfish toxins (PST) and Dinophysis spp. producing diarrhetic shellfish toxins (DST). Toxic species in genus Alexandrium distribute widely along the coast of China and intensive algal blooms of A. tamarense and/or A. catenella were found in the northern part of the Yellow Sea (YS), the sea area near the Changjiang River estuary in the East China Sea (ECS), and some bays in the South China Sea (SCS). Toxic Dinophysis spp. have been observed in all the China seas, and blooms of toxic Dinophysis spp. were reported in SCS and the northern part of YS, co-occurring with other microalgae. Proliferation of the toxic Alexandrium spp. and Dinophysis result in the contamination of shellfish products, and led to poisoning incidents sometimes. With the progress of high performance liquid chromatography (HPLC) and mass spectrometry (MS), more and more toxins were detected from the shellfish samples. The increasing awareness on toxic algal blooms and phycotoxins, as well as the rapid development of mariculture industry in China, require more studies on these issues.