In this paper, accumulation and distribution of microcystins (MCs) was examined monthly in six species of fish with different trophic levels in Meiliang Bay, Lake Taihu, China, from June to November 2005. Microcystins were analyzed by liquid chromatography electrospray ionization mass spectrometry (LC-ESI-MS). Average recoveries of spiked fish samples were 67.7% for MC-RR, 85.3% for MC-YR, and 88.6% for MC-LR. The MCs (MC-RR + MC-YR + MC-LR) concentration in liver and gut content was highest in phytoplanktivorous fish, followed by omnivorous fish, and was lowest in carnivorous fish; while MCs concentration in muscle was highest in omnivorous fish, followed by phytoplanktivorous fish, and was lowest in carnivorous fish. This is the first study reporting MCs accumulation in the gonad of fish in field. The main uptake of MC-YR in fish seems to be through the gills from the dissolved MCs. The WHO limit for tolerable daily intake was exceeded only in common carp muscle.