Since the beginning of this century, microRNAs (miRNAs), which are tiny RNA molecules, have become one of the major research topics on gene expression regulation in both animals and plants. The major task of miRNA study is to elucidate how the miRNAs are expressed in vivo, how they exert regulatory effects on their targets, and how they can be qualitatively or quantitatively cloned. For these purposes, the methodology of miRNA study has been developed and significantly improved in recent years. The focus here is on a number of powerful methods for plant miRNA research including bioinformatics tools and experimental approaches being used for upstream or downstream analysis of miRNAs or miRNA cloning. Some discrepancies exist in the miRNA research methodology between plants and animals, for example, 5' modified RACE (Rapid Amplification of cDNA Ends) can be used for cleavage target validation only in plants. However, numerous common methods are shared by these two miRNA research areas. Thus, this review will enhance our understanding of miRNA research methodology in organisms.