Microcystin-leucine-arginine (MCLR) is the most toxic and the most commonly encountered variant of microcystins (MCs) in aquatic environment, and it has the potential for developmental toxicity. A number of previous studies have described the developing toxicity of MCLR based on conventional toxicological indices. However, the molecular mechanisms by which it expresses its toxicity during the early development remain largely unknown. To further our understanding of mechanisms of action and identify the potential protein biomarkers for MCLR exposure, a proteomic analysis was performed on developing zebrafish embryos exposed to 0.5 mg/L MCLR until 96 hours post-fertilization. 2-DE combined with MS was employed to detect and identify the protein profiles. Results showed that 75 spots from the 0.5 mg/L MCLR condition showed a significant increase or decrease in abundance compared with the control. In total, 40 proteins were identified. These proteins were mainly included in process related to oxidative stress, energetic metabolism, and the cytoskeleton assembly. MCLR exposure also affects the expression of the subunits of protein phosphatases 2A. Furthermore, the proteomic and transcriptional analysis of nine proteins was determined by Western blot and quantitative real-time PCR due to their correlation with the known MCLR toxic mechanisms. The consistent and discrepant results between protein and mRNA levels indicated complicated regulatory mechanisms of gene expression in response to MCLR exposure.