Ciguatoxins (CTXs), a family of highly oxygenated transfused cyclic polyether ladder toxins, are produced by some toxigenic phenotypes of benthic dinoflagellates in the genera Gambierdiscus and Fukuyoa. The toxins are biotransformed and accumulated in coral reef fishes via the marine food chain, resulting in the most frequent non-bacterial seafood poisoning syndrome-termed ciguatera poisoning. Consumption of fish contaminated by CTXs has caused gastrointestinal, cardiovascular and neurological symptoms and occasionally death in human consumers. Ciguatera poisoning is currently considered a globally neglected disease. Affected by global climate change and human activities, the geographic expansion of benthic dinoflagellates is obvious, frequent ciguatera poisoning events especially in Asian regions, has posed a significant threat to human health and ecosystem health. This article reviews the research on key issues and scientific achievements on CTX-producing benthic microalgae, focusing on the species diversity, chemical diversity, physiological and ecological study of the ciguatera causative dinoflagellates and the mechanisms of biosynthesis, biotransformation and accumulation of CTXs. This review also highlights areas that deserve special research focus going forward in Asia regions which is the potential ciguatera outbreak areas to better protect the ecological safety and resident health.