Fish skin plays an important role in the mucosal immune response. In order to investigate the molecular mechanisms of mucosal immune responses in fish, the Crucian carp (Carassius auratus) were used as an animal model for fish skin immune system (FSIS), and proteomics analysis of protein expression in the skin of C. auratus was performed by using two-dimensional polyacrylamide gel electrophoresis (2-DE) combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF-MS) techniques. The results showed that 214 protein spots observed on 2-DE gels shared matching profiles of about 88% protein expression spots, while the 800 μg loading dose, and 18 cm pH3-10 IPG strips were used for isoelectric focusing (IEF) to 80 000 Vh. The 31 protein spots in the skin of fish were further identified as the 22 kinds of proteins by MS/MS analysis, namely myosin heavy chain, actin, keratin, zinc finger protein 585B, Rab15 effector protein, coiled-coil domain-containing protein 168, NCK1-associated protein, and creatine kinase M-type, enolase, pyruvate dehydrogenase E1 component subunit alpha, adenylate kinase isoenzyme 1, etc. Further analysis of protein functional classification based on Gene ontology (GO) showed 12 mainly biological processes, including metabolic process, cellular process, organism process, immune response, biological regulation and signaling etc.. The three of all biological processes such as metabolic, cellular and organism accounted for 24.7%, 19.5%, and 16.9% respectively, and immune response-related proteins included transformation/transcription domain-associated protein, keratin type I cytoskeletal 10, keratin type II cytoskeletal 8, and keratin type II cytoskeletal 6A. This is the first report on proteomics analysis of expressed proteins in the skin of C. auratus, and this study will help to understand the molecular mechanisms of mucosal immune responses at protein level in fish.