Gender differences in substrate selection have been reported during endurance exercise. To date, no studies have looked at muscle enzyme adaptations following endurance exercise training in both genders. We investigated the effect of a 7-week endurance exercise training program on the activity of beta-oxidation, tricarboxylic acid cycle and electron transport chain enzymes, and fiber type distribution in males and females. Training resulted in an increase in VO2peak, for both males and females of 17% and 22%, respectively (P < 0.001). The following muscle enzyme activities increased similarly in both genders: 3-beta-hydroxyacyl CoA dehydrogenase (38%), citrate synthase (41%), succinate-cytochrome c oxidoreductase (41%), and cytochrome c oxidase (COX; 26%). The increase in COX activity was correlated (R2 = 0.52, P < 0.05) with the increase in VO2peak/fat free mass. Fiber area, size, and % area were not affected by training for either gender, however, males had larger Type II fibers (P < 0.05) and females had a greater Type I fiber % area (P < 0.05). Endurance training resulted in similar increases in skeletal muscle oxidative potential for both males and females. Training did not affect fiber type distribution or size in either gender.