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6-Hydroxydopamine (6-OHDA), one of the most commonly used dopaminergic (DA) neurotoxins used as a model for Parkinson’s disease (PD) in vitro and in vivo, is likely to damage neurons through the generation of reactive oxygen species (ROS) such as the superoxide radical in mitochondria; however, details of the molecular events that occur in such a model are not available. In an attempt to identify the proteins involved in this process, we applied an iTRAQ-2D LC-MS/MS-based proteomic approach to analyze the protein profile of the 6-OHDA-induced PD zebrafish (Danio rerio) model. Zebrafish were exposed to 6-OHDA to selectively kill DA neurons. DA depletion was determined by whole mount immunostaining with antibody against tyrosine hydroxylase and was further validated by the detection of tyrosine hydroxylase (th) mRNA expression using quantitative real-time PCR. The change of zebrafish swimming behavior as a consequence of DA neuronal damage was monitored. In contrast to vehicle-treated healthy zebrafish, treatment with 6-OHDA induced DA neuronal loss, down-regulated th mRNA expression and significantly altered the swimming behavior of zebrafish. Our iTRAQ-2D LC-MS/MS analysis identified a total of 1,709 unique proteins from zebrafish lysates and bioinformatic analysis of the proteomic profile suggested the potential involvement of both TNF-α/NF-κB and oxidative phosphorylation pathways in 6-OHDA-induced neurodegeneration in zebrafish. These data emphasize the need for further research at the global protein level to unravel the underlying mechanism of 6-OHDA-induced neurotoxicity and the roles of the corresponding targets.