The development of the reproductive organs and the gametogenesis in animals are complex and multistage processes that require the precise and efficient regulation. In this review, we summarized the recent findings about the essential functions of microRNAs (miRNAs) in the regulation of gene expression during the differentiation of germ cells in spermatogenesis and oogenesis. Most likely, main and common functions of the conserved and highly expressed miRNAs in the male and female reproductive organs of mammals are the control of differentiation and proliferation of cells. Also we discussed a possible involvement of germline- expressed miRNAs in the formation of reproductive barriers and speciation.