The pathomorphogenesis of hypertrophic cardiomyopathy is a disruption of the arrangement of bundles of muscle cells in the myocardium and is associated with mutations in genes encoding the synthesis of myocardial contractile proteins. Metabolic changes in this pathology are caused by hypertrophy of the interventricular septum due to disruption of the myocardial contractile apparatus associated with these mutations, as well as mitochondrial dysfunction. Mutations in myofiber proteins can negatively affect mitochondria through increased oxidative stress due to increased ATP demand. Mitochondria are complex organelles with their own circular DNA, as well as the presence of enzyme complexes involved in redox reactions, which causes frequent damage to mitochondrial protein structures and membranes by reactive oxygen species. In this regard, mitochondrial dysfunction can also be caused by mutations in genes encoding mitochondrial proteins, which leads to disruption of mitophagy and mitochondrial dynamics. The functioning of defective mitochondria is associated with insufficient ATP synthesis and ineffective muscle contraction, which leads to the same consequences at the tissue level as mutations in contractile protein genes. In this review, we tried to summarize the role of mitochondrial dysfunction in the pathomorphogenesis of hypertrophic cardiomyopathy.