Gene assemblies are new technologies developed in recent years in the field of synthetic biology. They are based on large-scale analysis of genome sequences to find new or cryptic gene clusters which synthesize bioactive substances. The silent or cryptic gene clusters in microorganisms can be activated to synthesize potential valuable compounds by these technologies. We aim to elucidate the principle, the key strategy and the application of in vivo and in vitro gene assemblies. These technologies play an important role in synthetic biology, metabolic engineering and functional genomics and they will be of great value to efficiently produce bioactive compounds.