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Methylmercury (MeHg) is the most important and the most abundant organic Hg pollutant in the aquatic ecosystem that can affect human health through biomagnification. It is the most toxic organic Hg form, which occurs naturally and by human-induced contamination in water and is further biomagnified in the aquatic food web. MeHg is the only Hg form that accumulates in living organisms and is able to cross the blood–brain barrier, presenting an enormous health risk. Anthropogenic activity increases eutrophication of coastal waters worldwide, which promotes algae blooms. Microalgae, as primary producers, are especially sensitive to MeHg exposure in water and are an important entrance point for MeHg into the aquatic food web. MeHg assimilated by microalgae is further transferred to fish, wildlife and, eventually, humans as final consumers. MeHg biomagnifies and bioaccumulates in living organisms and has serious negative health effects on humans, especially newborns and children. Knowledge of the microalgae–MeHg interaction at the bottom of the food web provides key insights into the control and prevention of MeHg exposure in humans and wildlife. This review aims to summarize recent findings in the literature on the microalgae–MeHg interaction, which can be used to predict MeHg transfer and toxicity in the aquatic food web.