We tested the hypothesis that chronic endurance exercise is associated with the recruitment of four major upper airway muscles (genioglossus, digastric, sternohyoid, and omohyoid) and results in an increased oxidative capacity and a fast-toward-slow shift in myosin heavy chain (MHC) isoforms of these muscles. Female Sprague-Dawley rats (n = 8; 60 days old) performed treadmill exercises for 12 weeks (4 days/week; 90 minutes/day). Age-matched sedentary female rats (n = 10) served as control animals. Training was associated with an increase (p < 0.05) in the activities of both citrate synthase and superoxide dismutase in the digastric and sternohyoid muscles, as well as in the costal diaphragm. Compared with the control animals, Type I MHC content increased (p < 0.05) and Type IIb MHC content decreased (p < 0.05) in the digastric, sternohyoid, and diaphragm muscles of exercised animals. Training did not alter (p > 0.05) MHC phenotype, oxidative capacity, or antioxidant enzyme activity in the omohyoid or genioglossus muscle. These data indicate that endurance exercise training is associated with a fast-to-slow shift in MHC phenotype together with an increase in both oxidative and antioxidant capacity in selected upper airway muscles. It seems possible that this exercise-mediated adaptation is related to the recruitment of these muscles as stabilizers of the upper airway.