Introduction: Regular physical activity can lead to metabolic changes in adipose and bone tissue. In this study we hence investigated the effects of interval and continuous aerobic exercise on resting levels of adiponectin, leptin, osteocalcin and Tartrate resistant acid phosphatase 5b (TRACP 5b) in obese and overweight females. Materials and Methods: From among ninety obese and overweight healthy female students, 22 volunteer were randomly selected and investigated. Exercise programs included treadmill, 3 sessions per week for 8 weeks with interval exercise training, intensity 85-95% peak heart rate, for 33 minutes and continuous exercise training, intensity 50-70% peak heart rate, for 41 minutes. Data on blood samples using ELISA and anthropometrics and body composition were documented before and after 8 weeks. Results: results indicated that interval training significantly increased adiponectin (P=0.027) and decreased osteocalcin (P=0.047). In continuous training fat percent significantly decreased (P=0.014). Comparing groups, no significant difference was observed between groups in other factors. Conclusion: High-intensity interval training without any significant reduction in weight lead to increase in adiponectin and decrease in osteocalcin indicating that this type of exercise is associated with an increase in bone formation due to interaction of adiponectin and osteocalcin.