β-N-methylamino-L-alanine (BMAA) and 2,4-diaminobutyric acid (DAB) are two newly identified algal toxins, and they may react with chlorine to undergo decomposition and generate disinfection byproducts (DBPs) during pre-chlorination as well as chlorine disinfection. In this study, the decomposition of BMAA and DAB during chlorination and the consequent DBPs formation were investigated. The BMAA and DAB concentrations in source waters were determined, the decomposition kinetics of BMAA and DAB and the formation of DBPs during chlorination were studied, the formation pathways of DBPs from BMAA and DAB were explored, and the factors which may affect the decomposition and DBPs formation were examined. The results revealed that BMAA and DAB were commonly detected in source waters from Taihu Lake, and the highest level of BMAA reached 230.8 ng/L, while the concentrations of DAB were generally around 2.0 ng/L. The decomposition of BMAA and DAB during chlorination both followed pseudo-first-order decay while the decomposition rate constant of DAB was significantly higher than that of BMAA. Trihalomethanes (THMs), haloacetic acids (HAAs), and haloacetonitriles (HANs) were all generated during the chlorination of BMAA and DAB with relatively high yields. Notably, the THMs, HAAs, and HANs yields of each carbon atom from BMAA and DAB were significantly higher than that from other organic precursors, and the formation of HANs from DAB was significantly higher than that from BMAA. The formation pathways of DBPs from BMAA and DAB were tentatively proposed and verified through theoretical calculations. Of note, the proposed formation pathways of THMs and HAAs from BMAA were similar to that from DAB, while the proposed formation pathways of HANs from BMAA and DAB showed some differences. Chlorine dose, pH and temperature all affected the decomposition of BMAA and DAB and DBPs formation during chlorination.