Modified atmosphere packaging and controlled atmosphere storage (hypoxia conditions) extend shelf lives of horticultural products by depressing the O uptake rate. We investigated the relationship between atmospheres and alternative oxidase (AOX) to cytochrome c oxidase (COX) activities (on the basis of oxygen isotope discrimination) and the relative amounts of two respiratory enzymes, AOX and COX, during the early stage of storage. Broccoli florets, with high O uptake rates, were stored under hypoxia and normoxia at 25 °C. O uptake rates, weight loss, and yellowing of broccoli florets were significantly lower when stored under hypoxia than when stored under normoxia. Significantly more AOX proteins were produced during storage under normoxia, but COX proteins were more consistent than those of AOX proteins. Hypoxia may depress the expression of AOX and prolong the shelf life. Oxygen isotope discrimination was elevated under hypoxia after 50.5 h. AOX production in broccoli was controlled more by changing atmospheres than by COX.