The development of the reproductive organs and the gametogenesis of animals are complex and multistage processes that require the precise and effective regulation. In this review, we summarized the recent findings about essential functions of miRNAs in the regulation of gene expression during the differentiation of germ cells in spermatogenesis and oogenesis. Most probably, the main functions of the conservative and highly-expressed miRNAs in the reproductive organs of mammalian are the control of differentiation and proliferation of cells. Also we discussed the possible involvement of the germline-expressed miRNAs in the formation of the reproductive barriers and speciation.