Microalgae are rich resources for high-value nutrients and biodiesel production. However, extraction of these valuable compounds from them requires costly energy-consuming procedures due to their rigid cell walls. Application of cell-disruptive agents, the AES-Bt agents, extracted from an algicidal bacterium, Bacillus thuringiensis ITRI-G1, are a promising way to reduce the cost of cell disruption. Treatment with AES-Bt agents resulted in a rapid decline of photosynthesis ability and caused cell death in Chlorella vulgaris. Hallmarks of programmed cell death (PCD), including chromatin condensation, DNA fragmentation, and phosphatidylserine externalization, were detected in C. vulgaris cells treated with the AES-Bt agents. Therefore, the cell disruption effect caused by application of the AES-Bt agents can be due to the occurrence of PCD. Similar to other PCDs, the PCD caused by AES-Bt agents was also associated with increased reactive oxygen species (ROS). However, co-treatments with diphenyleneiodonium chloride (DPI), an NAD(P)H oxidase inhibitor, or N,N'-dimethylthiourea (DMTU), a hydrogen peroxide (H2O2) trap, with the AES-Bt agents successfully reduced ROS production, and more cells displayed a feature of PCD detected after the co-treatments. In conclusion, the AES-Bt agents can promote PCD of microalgae; however, the mechanism may not be through induction of ROS.