Mitochondria play a crucial role in energetic metabolism, signaling pathways, and overall cell viability. Mitochondrial dysfunctions are known to cause a wide range of human diseases that affect tissues especially those with high energetic requirements, such as skeletal muscle, heart, kidney, and central nervous system, while being involved in cancer, aging, and metabolic processes. At the same time, the microRNA (miRNA) gene family has been demonstrated to be involved in most cellular processes through modulation of proteins critical for cellular homeostasis. Given the broad scope of reactivity profiles and the ability of miRNAs to modify numerous proteomic and genomic processes, new emphasis is being placed on the influence of miRNAs at the mitochondrial level. Recently, the localization of miRNAs in mitochondria was characterized in different species. This raises the idea that those miRNAs, noted “mitomiRs,” could act as “vectors” that sense and respond dynamically to the changing microenvironment of mitochondria at the cellular level. Reciprocally, we present the involvement of mitochondria in small RNA biogenesis. With the aim of deciphering the significance of this localization, we discuss the putative mechanism of import of miRNAs at mitochondria, their origin, and their hypothetical roles within the organelle.