In recent years, owing to the intensified human activities, a large number of nutrients, primarily nitrogen and phosphorus, flow into lakes and other water bodies and result in serious eutrophication. However, the cultural eutrophication is often associated with cyanobacteria blooms which can create significant water quality and human health problems. What's more, some species of cyanobacteria are capable of producing secondary metabolites named cyanotoxins. Mass populations of toxin-producing cyanobacteria are in natural and controlled water bodies include blooms and scums of planktonic species, and mats and biofilms of benthic species. Toxic cyanobacterial populations have been reported in freshwaters in over 45 countries. These toxins can be classified into five main types according to their mechanism of action in vertebrates: hepatotoxins, cytotoxins, dermatotoxins, neurotoxins and irritant toxins. These toxins (microcystins, nodularins, saxitoxins, anatoxin-a, anatoxin-a(s), cylindrospermopsin) are structurally diverse and their effects range from liver damage, including liver cancer, to neurotoxicity. There are more than 80 microcystin congeners, microcystin-LR (L, L-leucine; R, L-arginine) is the best studied cyanobacterial toxin, whereas information for the other toxins is largely lacking. Many studies on the effects of cyanobacteria and their toxins over a wide range of aquatic organisms, including invertebrates and vertebrates, have reported acute effects (e.g., reduction in survivorship, feeding inhibition, paralysis), chronic effects (e.g., reduction in growth and fecundity), biochemical alterations (e.g., activity of phosphatases, GST, AChE, proteases), and behavioral alterations. Research has also focused on the potential for bioaccumulation and transferring of these toxins through the food chain. In general, the toxins can transfer to human bodies by drinking and very little by entertainment or health care products. In some special circumstances, the toxins can also be transferred into human bodies by dialysis. Be the highest level of the food chain, toxins can also transfer to human beings by eating aquatic products. As an important part of the aquatic ecosystem, zoobenthos plays an important role in the aquatic food web. On the one hand, it plays an important part in the material and energy flow process. It is not only the source of the predacity fish, but also the predator of the phytoplankton, zooplankton or organic detritus. On the other hand, some species of the zoobenthos can also be used in water cleaning and influence the formation of the eutrophication. The most important thing is that many of them are even closely related to human beings (directly or indirectly food sources), especially the people leave around the lakes and other water bodies, so the study of the cyanotoxin toxicology of zoobenthos is of great importance. In this review, we first summarized the mechanism of toxicity of cyanotoxin on zoobenthos on the base of a brief introduction of cyanotoxins, with emphasis on microcystins. Secondly, the effects of cyanotoxins on zoobenthos is discussed in details, including the bioaccumulation and elimination of the cyanotoxin, the effects of cyanotoxin and the food web studies about cyanotoxin (mainly microcystis) in zoobenthos. At last, we prospect the further research directions as well as drawbacks and future needs in this field of research.