In recent years, cyanobacterial blooms have dramatically increased and become an ecological disaster worldwide. Cyanobacteria are also known to produce a wide variety of toxic secondary metabolites, i.e. cyanotoxins. Microcystins (MCs), a group of cyclic heptapeptides, are considered to be one of the most common and dangerous cyanobacterial toxins. MCs can be incorporated into the cells via organic anion transporting polypeptides (Oatps). It’s widely accepted that inhibition of protein phosphatases (PPs) and induction of oxidative stress are the main toxic mechanisms of MCs. MCs are able to induce a variety of toxic cellular effects, including DNA damage, cytoskeleton disruption, mitochondria dysfunction, endoplasmic reticulum (ER) disturbance and cell cycle deregulation, all of which can contribute to apoptosis/programmed cell death. This review aimed to summarize the increasing data regarding the intracellular biochemical and molecular mechanisms of MC-induced toxicity and cell death.