This study investigated the effects of acute exercise and menstrual phase on adiponectin and osteocalcin concentrations, and the possible role of these biomarkers in exercise-induced substrate oxidation in rowers. Thirteen female rowers (19.3 ± 2.3 years; height: 172.7 ± 3.9cm; body mass: 66.5 ± 7.9kg) performed 1-h rowing ergometer exercise at 70% of maximal oxygen consumption (VO2max) during follicular phase and luteal phase of the menstrual cycle. Oxygen consumption (VO2), total energy expenditure (EE), carbohydrate EE, and lipid EE were assessed during the exercise. Venous blood samples were collected before and after ergometer exercise. No differences (p > 0.05) were observed in substrate oxidation values during exercise across menstrual cycle. Exercise resulted in an acute rise in osteocalcin and no changes in adiponectin at both menstrual cycle phases. Adiponectin and osteocalcin were not related across phase or time (r < 0.211; p > 0.05). Post-exercise adiponectin was related (p < 0.05) to mean VO2 (r = 0.459) and total EE rate (r = 0.598), while post-exercise osteocalcin was correlated (p < 0.05) with mean total (r = 0.411) and lipid (r = 0.557) EE rates. In conclusion, menstrual cycle phase had no effect on substrate oxidation, and adiponectin and osteocalcin responses to acute exercise. It appears that adiponectin and osteocalcin may serve as signals for metabolic reaction to the energy cost of the acute exercise in female rowers.