Some free fatty acids are toxic to phytoplankton, and the toxic effects are multiple. However, precisely how they kill phytoplankton is debatable. Here we show that fatty acids result in damage to plasma membranes, which might account for their lethal effects on phytoplankton. In this study, we used two chlorophytes (Chlorella vulgaris Beij. and Monoraphidium contortum (Thur.) Kom.-Legn.) and a cyanobacterium (Anabaena P-9) as test organisms. When these organisms were treated with deleterious concentrations of fatty acids, a remarkable elevation of extracellular potassium (K+) was detected in the culture medium; this indicates that leakage of intracellular K+ occurred as a result of damage to the plasma membranes. Exposure to unsaturated fatty acids resulted in higher levels of leaked K+ than did exposure to saturated ones, and levels of leakage displayed a positive correlation with the susceptibility of the growth of organisms to fatty acids. Stressed phytoplankton cells also exhibited cell lysis followed by free release of phycobilins. The sequence of cytotoxic effects elucidated here suggests that fatty acids primarily affect the plasma membranes, leading to a change in membrane permeability and dissociation of phycobilins from the thylakoids. Severe damage to the plasma membranes would give rise to a disruption of the stressed cells.