The amount of microcystin in Microcystis aeruginosa bloom was investigated during the rainy season of 1999 in Laguna de Bay, the Philippines. Bloom samples taken from the West Bay and East Cove stations of the lake were studied in relation to the characteristics of environmental conditions. Four types of microcystins, microcystin-LR (MC-LR), microcystin-RR (MC-RR), 6(Z)-Adda-microcystin-RR, and 3-desmethylmicrocystin-LR were identified from the natural bloom samples among which MC-LR was the most dominant type of microcystin. Production of microcystin (88.6 µg/100 mg dried cells) was highest during the first sampling week that coincided with high water transparency and high conductivity. The occurrence of a strong typhoon during the second sampling week had changed the environment drastically, which was characterized by low water transparency, high turbidity, low water temperature, and with trace amounts of MC-LR detected at the East Cove station. Thus, toxin production over time as well as the relationship between Microcystis production and toxin concentration could not be fully evaluated.