As the genome sequencing of human and other species is complete, a major task in life science is to elucidate biological functions of thousands of genes. Life cycle of human and animals starts from single fertilized eggs that will develop step by step into sophisticated organisms consisting of multiple tissues and organs. During embryogenesis, genes are expressed sequentially according to inherent programs and gene products function coordinately, which determine and actualize the body plan. Functional genomics of embryos can be accelerated if an appropriate model animal is exploited. Zebrafish is an excellent model for such a study. The natural advantages of Zebrafish include high production of eggs, external development of embryos, small size and easy maintenance. In addition, many molecular, cellular, embryonic and genetic operations can be done easily in zebra fish. Two approaches, forward and reverse genetics, have been widely used to study gene functions during development of zebrafish embryos. The forward genetics is to identify genes from mutants created by mutagenesis with chemical mutagens, y-ray and recombinant retrovirus. More than 4,000 mutants with various embryonic defects have been generated and about 500 genes responsible for mutant phenotypes have been identified. The mutagenesis in zebrafish has revealed some important mechanisms controlling development of vertebrate embryos. With respect to reverse genetics approach, over 3,000 tissue-specific genes have been identified through whole-mount in situ hybridization screen. The functions of some of these genes during embryogenesis have been studied in details.