The pelagophytes Aureococcus anophagefferens and Aureoumbra lagunensis have formed ecosystem disruptive algal blooms in shallow estuaries of the United States and South Africa for more than two decades. The largescale brown tide events in the coastal waters of Hebei Province in recent years make China the third country that is affected by brown tide in the world. These algae are able to utilize a wide variety of organic nutrients and achieve high growth rates at low light and nutrient levels. They have significant negative impacts on the shellfish mariculture industry, economy and recreational industry. We review research progress in the last two decades on morphology, physiology and molecular and genomic characteristics of these brown tide algae, especially the genes that encode many of the key proteins that facilitate bloom formation and persistence. Moreover, the research progress in China about brown tide is summarized. The prospects of the research on brown tide are also discussed.