Zebrafish (Danio rerio) is becoming more and more popular as a model organism to study vertebrate organogenesis and regeneration, taking the advantage of its extra-uterine development, transparency, strong regeneration ability and suitability for the large scale genetic screen. In the past decades, a series of useful methods have been established in zebrafish, which allows studies of important questions in developmental biology including cell fate determination, differentiation, morphogenesis, and regeneration after tissue/organ injury. Recently, using large scale mutagenesis screen and improved live imaging techniques, many questions that had not been well understood in mice have been successfully investigated in zebrafish. Therefore, we are confident that the zebrafish model system will further help decipher the cellular and molecular mechanisms of organogenesis and regeneration in the future, providing valuable references for the treatment of related clinical diseases. This review just summarized the progress in the studies of the important organs development using zebrafish, such as central nervous system(CNS), liver and pancreas, blood and vessel, recently. Meanwhile, the updated informations about the regeneration of tail fin, heart, liver, retina and so on in zebrafish were also included in this paper.