Abstract <p>Variability of the mitochondrial cytochrome <i>c</i>-oxidase I (mtDNA) gene fragment is negatively associated with body size of roach <i>Rutilus rutilus</i> (L., 1758), and bream <i>Abramis brama</i> (L., 1758), and is the cause of intergenomic conflict in hybrids with highly polymorphic mtDNA of roach. Different aerobic requirements due to differences in body size between roach and bream may have increased the selection of co-adapted mitochondrial–nuclear genes for ATP production and led to divergence of species in locomotor activity and neural processes. These differences may be related to the rate of free radical leakage (ROS), which is set by the apoptotic threshold and is linearly related to the rate of change in COX1. The roach has a smaller body size, higher motor and feeding activity, and a low threshold of excitability, which determines the interspecies differences of behavioral reactions with bream without a predator and in the presence of a low-active predator. The high rate of changes in COX1 and ROS leakage in roach allow to tolerate the suboptimal correspondence of mitochondrial–nuclear respiratory complexes for ATP production and to reduce the threshold of excitability of the nervous system. Intergenomic conflict, which manifests itself in hybrids ♀<i>R. rutilus</i> × ♂<i>A.&#xa0;brama</i> by a violation of the inheritance of greater body length from the male bream, does not affect the maternal effect of behavioral traits. Whereas high genomic compatibility leads to an increase in boldness (ROS threshold), the strength of the excitatory process, and the similarity of hybrids ♀<i>A. brama</i> × ♂<i>R. rutilus</i> with the male roach in terms of motor activity, which may be a consequence of remodeling of energy metabolism due to the inheritance of the roach body length. However, under stress conditions, the curve of the dynamics of the behavior of AR hybrids is similar to <i>A. brama</i>, but hybrids can no longer quickly reduce the metabolic rate to zero, like bream.</p>