Although the massive sequencing of mitochondrial DNA from various organisms, together with studies of a different nature, has contributed enormously to the knowledge of the organization and function of this cytoplasmic genome, many issues, mainly the relationships with the nuclear genome, remain unsolved. This review critically evaluates the most recent advances in research on the evolution of the mitochondrial DNA from a qualitative and quantitative point of view, underlining the multiplicity of structures and genetic organization of this genome, which contrasts with its reduced, but rather constant, information content in various organisms. It also highlights the role that mitochondrial DNA is now playing, particularly in metazoans, in different disciplines and application fields. Among these, particular attention is focused on the discovery of the mitochondrial origin of several diseases affecting primarily the neuromuscular system.