Mass propagation of algae in drinking water source affects the coagulation process in water treatment systems. Many researchers indicated that some kinds of algal organic matters (AOMs) interacted with coagulants by coordinate bonds and brought about several disorders due to the increase in both the coagulant demand and the residual coagulant in treated water. However, the inhibitory mechanism on the coagulation by AOMs has not been fully elucidated. In this study, AOMs able to form complex with aluminium coagulant were isolated and analyzed. The results of the gel chromatography showed that extracellular organic matters (EOMs) from Microcystis aeruginosa (NIES-91) have molecular weight of between 10 and 20 kDa, around 40 kDa and more than 600 kDa. The amount and diversity of EOMs increased as the algal growth. AOMs able to form complex with aluminium coagulant were successfully isolated with the affinity chromatography. SDS-PAGE analysis revealed that these AOMs included proteins that have molecular weight between 43 and 67 kDa. Since several kinds of proteins such as metallothionein are known for strongly adsorbing multivalent cations, the isolated algal proteins able to form complex with aluminium might have a high capacity of capturing coagulants and inhibit the coagulation in the drinking water treatment.