In the mitochondrial F(O)F(1) ATP-synthase/ATPase complex, subunits α and β are part of the extrinsic portion that catalyses ATP synthesis. Since there are no reports about genes and proteins from these subunits in crustaceans, we analyzed the cDNA sequences of both subunits in the whiteleg shrimp Litopenaeus vannamei and their phylogenetic relationships. We also investigated the effect of hypoxia on shrimp by measuring changes in the mRNA amounts of atpα and atpβ. Our results confirmed highly conserved regions for both subunits and underlined unique features among others. The ATPβ deduced protein of shrimp was less conserved in size and sequence than ATPα. The relative mRNA amounts of atpα and atpβ changed in shrimp pleopods; hypoxia at 1.5 mg/L caused an increase in atpβ transcripts and a subsequent decrease when shrimp were re-oxygenated. Results confirm that changes in the mRNAs of the ATP-synthase subunits are part of the mechanisms allowing shrimp to deal with the metabolic adjustment displayed to tolerate hypoxia.