MicroRNAs, a type of small non-coding RNA specialized in regulation of gene expression, extensively participate in biological development, cell differentiation, apoptosis, and other cellular processes. MiRNAs evolved independently in different strains and generally conserved in the process of evolution. This review summarized the origin, regulation of methylation, and evolutionary conservation of miRNAs. In addition, application of miRNAs in diseases, animals and plants was discussed.