Introduction: A recent over expression model demonstrated that peroxisome proliferator-activated receptor coactivator 1-alpha (PGC-1α) regulates the expression of fibronectin type III domain containing protein 5 (FNDC5); a novel myokine with a potential role in stimulating brown-fat-like development in white adipose tissue. The aim of this study was to investigate the effects of eight weeks of aerobic training with different intensities on FNDC5 protein in soleus muscle tissue of obese male Wistar rats. Methods: 24 adult rats (weight: 250 to 300 gr, BMI >30g/cm2) were divided into three groups: aerobic training with 70 to 75% Vo2max (moderate intensity), aerobic training with 80 to 85% Vo2max (high intensity) and, control group. All training groups carried out exercise training for 8 weeks running on treadmill (5 sessions/per-week for 60 min per session). After the training period, the level of FNDC5 protein was measured. Statistical test of ANOVA was used for data analysis to determine the difference between groups and post hoc test of Tukey was used for paired comparisons (p≤0.05). Results: The levels of FNDC5 in soleus muscle tissue in both moderate intensity and high intensity aerobic training group increased significantly (P=0.001). Conclusion: According to the results, increasing of FNDC5 as a result of eight weeks of moderate and high intensity aerobic training with moderate and high intensity, it seems that FNDC5 can mediate conversion of white to brown tissue and so affect losing weight and thermogenesis. Manuscript profile