A liquid chromatography electrospray mass spectrometry (LC/ESI/MS) method has been developed to identify and quantify microcystins in fish liver and intestine. Microcystins (MCs) were extracted from 500mg sample with methanol–water (85:25, v/v) and the extracts concentrated to 250μl. The parameters were optimized by a full factorial 2 3 design. Neither laborious pre-treatment nor clean up were necessary. MCs were separated using conventional C 18 column and an acetonitrile–acidified water (pH 3) gradient. Negative samples (without MCs) were discriminated by liquid chromatography diode array detection (LC/DAD). The limits of detection (LOD) and the limits of quantification (LOQ) resulted equal for MC-RR, MC-YR, and MC-LR and were 0.1 and 0.5μgg −1 , respectively. MCs recoveries at three levels in spiked samples (0.5–3.0μgg −1 ) were >92%, with relative standards deviations (RSDs) <16% for liver samples and >68% with RSDs <18% for intestine samples. The proposed method was applied to determine MC-LR in exposed fish to evaluate the bioaccumulation risk. The results showed the transference of MC-LR from cyanobacterial cells to fish tissues.