The increasing occurrence of cyanobacterial blooms in eutrophic water bodies has now caused worldwide concerns, which may cause adverse effects on the health of aquatic animals. Microcystins (MCs), a family of cyclic peptides, are the most widespread hepatotoxic toxins. This review details the effects of the MCs on fish, and discusses hotspots of future research. In early life stages, exposure to MCs causes, in a dose-dependent manner, perturbations to embryonic hatching, increasing malformation rate and decreasing survival rate. In adults, field and experimental studies demonstrated that MCs accumulate mainly in liver, but can also be found in muscle, intestine and other tissues. Histopathological damages in the liver, intestine, kidneys, heart, brain and gills were observed. Microcystin exposure also has been shown to affect growth rate, modify behavior and enzyme activities. In addition, MCs may have potential immunotoxicity. The detoxication mechanism of MCs in fish begins with a conjugation reaction to glutathione catalyzed by glutathione S-transferases. Further studies are needed to clarify the transport and molecule mechanism of MCs in fish, and the ecological impacts of MCs accumulation in aquatic food chains.