Abstract: A bloom of Microcystis aeruginosa occurred in a homestead pond in Rupgoanj, Dhaka. Bloom sample was collected and filtered through a glass fiber filter. Methanol-water extract of filtered cells were analyzed by High Performance Liquid Chromatography (HPLC) with UV, MS and MS-MS detection, detected three types of microcystins viz., Microcystin-RR, Microcystin-YR and Microcystin-LR and those were confirmed by HPLC-MS. The amount of MC-LR was the highest (34.8 μg L-1) followed by MC-RR (16.8 μg L-1) and MC-YR (10.9 μg L-1). The concentration of microcystins was well above the WHO provisional guideline value of 1 μg L-1 MC-LR. Further investigations need to characterize other types of microcystins from bloom forming cyanobacteria and their effect on human health and cultured fish in Bangladesh.