Microcystin-LR (MC-LR) is the most common hepatotoxic cyanotoxin produced primarily by . Although deaths from microcystin toxication have widely been attributed to hypovolemic shock due to hepatic interstitial hemorrhage, so far, information on coagulation factors of MC-LR has been rare. In our present study, the effects of MC-LR on the coagulation factors expression and pathological changes in zebrafish were investigated. Adult zebrafish were injected intraperitoneally with 200 μg/kg MC-LR and newly hatched larvae were placed in glass wares containing 200 μg MC-LR/L, liver and whole larvae were collected after exposure for 12 h, 24 h, 48 h and 96 h, respectively. mRNA levels of coagulation factor IX (FIX), coagulation factor VII (FVII) and coagulation factor VIIi (FVIIi) in liver of adult fish and total zebrafish larvae were analyzed using quantitative real-time PCR. Significant depression of FIX and FVII were observed in adult zebrafish at different time point, and FVIIi were also significantly decreased except for 12 h post-injection. In addition, the histopathological changes in adult zebrafish liver were observed, and the severe hepatic injuries were found at 96 h. The pathological changes further explained the transcriptional results. The transcriptions of FVII were significantly depressed throughout the entire experiment in zebrafish larvae, and the FIX only significantly depressed after exposure for 48 and 96 h, however, FVIIi just was significantly reduced after 12 h and 24 h stimulation. Whatever the mechanism, the effects of MC-LR on the transcription of these coagulation factors might explain the intrahepatic hemorrhage in liver after exposure to MC-LR, and which would provide new information to elucidate the hepatotoxicity of MC-LR.