The epimorphic regeneration of zebrafish caudal fin is rapid and complete. We have analyzed the biomechanism of zebrafish caudal fin regeneration at various time points based on differential proteomics approaches. The spectrum of proteome changes caused by regeneration were analyzed among controls (0 h) and 1, 12, 24, 48, and 72 h postamputation involving quantitative differential proteomics analysis based on two-dimensional gel electrophoresis matrix-assisted laser desorption/ionization and differential in-gel electrophoresis Orbitrap analysis. A total of 96 proteins were found differentially regulated between the control nonregenerating and regenerating tissues of different time points for having at least 1.5-fold changes. 90 proteins were identified as differentially regulated for regeneration based on differential in-gel electrophoresis analysis between the control and regenerating tissues. 35 proteins were characterized for its expression in all of the five regenerating time points against the control samples. The proteins identified and associated with regeneration were found to be directly allied with various molecular, biological, and cellular functions. Based on network pathway analysis, the identified proteome data set for regeneration was majorly associated in maintaining cellular structure and architecture. Also the proteins were found associated for the cytoskeleton remodeling pathway and cellular immune defense mechanism. The major proteins that were found differentially regulated during zebrafish caudal fin regeneration includes keratin and its 10 isoforms, cofilin 2, annexin a1, skeletal ␣1 actin, and structural proteins. Annexin A1 was found to be exclusively undergoing phosphorylation during regeneration. The obtained differential proteome and the direct association of the various proteins might lead to a new understanding of the regeneration mechanism. Molecular & Cellular Proteomics 11: 10.1074/mcp.M111.014118, 1-19, 2012.Regeneration is an important mechanism found among most of the animals including humans in various tissues and organs towards growth, regrowth, repair, reproduction, and survival. The biomechanism of regeneration has been widely studied but poorly understood because of its different extents in various animals. Understanding the basic molecular mechanism of regeneration in the wound environment is of high significance, because it can lead to an applied possibility of making nonregenerating to a regenerating system.Tissue regeneration in vertebrates is found with extensive capabilities. Regeneration of limbs in urodele and caudal fin in zebrafish are the most projected regeneration studies among vertebrates. Zebrafish regenerates a wide variety of tissue structures including heart, fin, spinal cord, and optic nerve (1-3) based on the characteristic regeneration mechanism involving epithelialization, mesenchymal disorganization, blastema formation, regenerative outgrowth, and termination.A great number of gene families, counting wnt, hox, fgf, fgfr, and msx genes, were shown to...