MicroRNAs (miRNAs) form a large class of small regulatory RNAs in eukaryotes. Although they share a common processing pathway and certain structural features, in general, there is no detectable sequence similarity among miRNAs from a given organism. On the other hand, many miRNAs are members of a family of a few, often very similar, paralogs. It is, thus, of interest to trace the evolutionary history of individual miRNAs, to identify the timing of gene duplications, and to study relationships between the histories of different miRNA families. Some miRNAs are transcribed from polycistronic primary transcripts. In these cases, we will study the evolution of entire clusters.