MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression and thus control diverse biological processes. The high interest in miRNAs as an important mediator of post-transcriptional gene regulation has led to the discovery of miRNAs in several organisms. The present article outlines and discusses the current status of miRNAs information on the basal chordate amphioxus and the evolution of miRNAs in metazoans.