In nature, seasons may be more reliably announced by changes in photoperiod than in temperature. To evaluate the role of day length in setting oxidative capacities of trout muscle mitochondria, we acclimated trout to summer (15 °C, 16L:8D), winter (5 °C, 8L:16D) and mixed conditions (15 °C, 8L:16D). Maximal oxidative capacities of isolated mitochondria at 5 and 15 °C were higher in mixed than summer conditions and higher again in winter conditions. At 5 °C, state 4 rates changed little with acclimation state whereas at 15 °C state 4 rates were lower in summer than in mixed or winter conditions. Using concentrations of the adenylate nucleotide translocase as the denominator for these rates gave much the same conclusions. By using inhibitors to block flux at specific points in the electron transport chain, we found that flux through Complexes II–IV was lowest in summer acclimated trout, increased upon acclimation to mixed and to winter conditions. Flux through complex IV was similar in trout acclimated to summer and mixed conditions, but increased significantly with acclimation to winter conditions. Flux through complex IV was 1.5 fold higher than state 3 rates for summer-acclimated trout but was similar to state 3 rates in trout acclimated to mixed or winter conditions. Our results indicate that a reduction in day length initiates increases in mitochondrial oxidative capacity typically associated with cold acclimation and that acclimation to both cold temperatures and short day lengths enhanced these changes. The overall similarity of the responses of state 3, of flux through complexes II–IV and of flux through complex IV suggests that a generalised mechanism such as changes in the phospholipid composition of the inner mitochondrial membrane may coordinate these changes.