Chlorine is often employed to dispose cyanobacteria-laden waters for inactivating cells or improving its removal efficiency. However, previous studies mostly focused on cyanobacterial blooms occurring in the exponential or stationary phase, and thus, cyanobacterial characteristics in the unblooming stage (lag phase) and their influence on chlorination were not well understood. Herein, Microcystis aeruginosa in late lag and exponential phases with the same cell density were selected to simulate unblooming and blooming stages, respectively, and their response to chlorination was investigated. Compared with the exponential phase, results showed that cyanobacteria in the late lag phase consumed lower chlorine but produced higher intracellular reactive oxygen species (ROS). Then, higher rate constants of photosynthetic activity inactivation (k f ) and membrane damage (k m ) were found in the late lag phase. Chlorine of >1.0 mg L −1 could degrade microcystin in this phase, and microcystin could be oxidized to below 1.0 μg L −1 by 2.0 mg L −1 chlorine. Besides, lower extracellular dissolved organic carbon (DOC), UV absorbance at 254 nm (UV 254 ), and their variation range were also observed in the late lag phase. These findings indicated that the chlorination performance in the two phases is different, and thus, it is necessary to reduce the applied dosage of chlorine to treat cyanobacterialaden source waters in the (late) lag phase.