The origins and evolution of metazoa(metazoans) traditionally studied on their comparative morphology and embryology are important issues in animal biology, palaeontology and evolutionary biology. As the successive progress and universally application of molecular genetics and molecualr developmental biology in these study areas, it is possible to clarify the phylogenetic relationships of all groups of metazoans on their genetic and developmental mechanisms. In this paper, we reviewed the molecular phylogeny and discussed the existing problems in metazoan studies, meanwhile, we are also oversighting the studies of matazoan evolution in the future.