Previously we have shown, using two-dimensional electrophoresis, that mitochondrial ATP synthase (F_oF₁-ATPase) ß-subunit is the 55-kDa protein increased in cold-acclimated carp Cyprinus carpio (Kikuchi K., Itoi S, and Watabe S, Fisheries Sci 65: 629-636, 1999). To clarify the coordinate expression in various subunits of carp F_oF₁-ATPase with temperature acclimation, we examined the differences in mRNA levels of mitochondrial proteins encoded by both nuclear and mitochondrial genes in fast muscle of carp acclimated to 10 and 30^°C. The mRNA levels of nuclear genes per unit weight of total RNA were nearly two fold higher in the 10^°C- than 30^°C-acclimated carp. However, the transcripts of mitochondrial genes for the 10^°C-acclimated carp in terms of the same comparing unit were 6- 7 times as much as those for the 30^°C-acclimated carp. The F_oF₁-ATPase activities measured at 10, 25 and 30^°C were nearly two fold higher for the cold-acclimated fish than their warm-acclimated counterparts. Such quantitative and qualitative changes in carp F_oF₁-ATPase may contribute to extra ATP production required to compensate for energy balance at suboptimal temperatures.