Currently, the issue of the aetiology of mitochondrial diseases resulting from mitochondrial DNA (mtDNA) defects is underestimated. Genetic research is mostly focused on alterations in the nuclear genome (nDNA), and its impact on disease development as well as further health consequences without considering mtDNA abnormalities. However, in the case of energy-dependent diseases, it is important to understand the bioenergetic pathophysiology and its relation with mtDNA changes. In the current animal research, there is limited data about mtDNA defects and their association with the development of bioenergetic diseases in the domestic dog (Canis lupus familiaris) in contrast to human medicine, where mitochondrial genetics research has recently increased. Molecular findings about mtDNA indicate that improper functioning of mitochondria resulting from genetic defects of mtDNA has a severe impact on cells and tissues, especially those that are heavily dependent on oxidative metabolism such as the brain, skeletal and cardiac muscles and, consequently, the whole organism. The aim of this paper is to highlight the role of defects of mitochondria and mtDNA on the development and course of different diseases in the domestic dog. The field of canine mitochondrial genetics and genomics is definitely inexhaustible, and it is worth drawing attention to the importance and consequences of the mitochondrial genome alterations. This review collects scientific data on mitochondrial DNA with special regard to the structure, features of canine mtDNA, and abnormalities in the mitochondrial genome and their association with the course and development of diseases, including mitochondrial myopathies, encephalopathies, and tumours.