It is well known that fish have stronger tolerance than mammals to microcystin (MC) exposure, and such a difference is attributed to their different core body temperatures. However, no in vivo study has been conducted to investigate the effects of temperature on MC-induced toxicity in fish, a typical poikilotherm. Tolerance and detoxification response of zebrafish treated with MC-LR were investigated under three temperatures. The LD50 values evidently increased with a decline of the temperature (547, 260 and 176 µg kg−1 at 12, 22 and 32 °C, respectively), indicating stronger tolerance of the fish at lower temperatures. Changes in the transcription of glutathione S-transferase (GST) isoforms in the fish were observed, and their sensitivity of response in the transcription of GST mRNA was on the order of 12 > 32 > 22°C. We screened out several GST genes which were more delicate to solve the MC-LR exposure at different temperatures, i.e. GST rho1, al, p1 and theta1 in the 12 °C group, and GST zeta1 and p2 in the 22 and 32 °C groups. Our findings partly validate the hypothesis that high temperature enhances toxic effects of MCs on poikilotherms. Our studies also indicate that temperature-dependent toxic effects should be taken into account for field toxic assessment of microcystins in fish. Copyright © 2010 John Wiley & Sons, Ltd.