Hypoxia commonly occurs in aquatic habitats and puts strong pressure on the benthic sessile organisms unable to escape the oxygen fluctuations. Here we focused on the effects of hypoxia/reoxygenation (H/R) on activities of the mitochondrial Complexes I and IV in hypoxia-tolerant marine bivalves, namely, the blue mussel Mytilus edulis, the Arctic quahog Arctica islandica and the Pacific oyster Crassostrea gigas, exposing them for one or six days to extreme hypoxia (<0.1% O2) followed by one hour of reoxygenation. Furthermore, we examined the potential role of the posttranslational modifications (PTM) by reversible protein phosphorylation in regulation of the Complex I and IV activities and in the mitochondrial responses to H/R stress. The overall level of protein phosphorylation by PKA (serine/threonine protein kinase A) and PKC (protein kinase C) was measured to test for possible association between the H/R-induced changes in the PKA and PKC activities and the respective protein products of these kinases. Our results showed a strong species-specific modulation of the PKA and PKC activities by H/R stress. In the mussels and quahogs, phosphorylation by PKA and PKC led to an increase in activity of Complexes I and IV, whereas in oysters these enzymes were insensitive to PKA and PKC activation. Non-site-specific dephosphoryaltion strongly suppressed the activity of Complex I and IV in all three studied species.