•Mitochondrial DNA (mtDNA) alterations are associate with canine development of diseases.•Mitochondrial diseases are highly heterogenic conditions induced by many factors.•The majority of mtDNA defects are canine mitochondrial myopathies, encephalopathies, and tumours.•More attention should be paid to the proper diagnosis of animals suffering from mitochondrial diseases.•There is a need to develop reliable molecular testing to confirm unambiguously the cause of development of canine mitochondrial diseases. 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.