Exercise-induced skeletal muscle adaptation requires degradation of cellular components carried out by autophagy. However, the alteration of autophagy by different intensity of exercise in skeletal muscle is still unknown. In the present study, we investigate whether low, moderate, and high-intensity exercises have different impacts on autophagy gene expression in gastrocnemius and soleus muscles of wistar rats. This work is limited because only rats are used, and does not cover human tissues. Twenty male wistar rats were assigned to four groups: sedentary control, low-intensity (LI, 10 m/minute), moderate-intensity (MI, 20 m/minute), and high-intensity (HI, 30 m/minute) exercises. Training was conducted 30 minutes/day with a 5 times/week interval for 8 weeks. RNA and protein were extracted from gastrocnemius and soleus muscles then stored in -80°C. Specific primers and antibodies for autophagy genes and protein levels were utilized for semi-quantitative PCR and Western Blot. Exercises decrease expression of autophagy gene LC3 (LI and MI 0.7 fold, HI 0.8 fold, p < 0.05) in gastrocnemius muscles and soleus muscle (LI, MI, and HI 0.8 fold, p < 0.05) compared to control. On the other side, we observed p62 gene expression decreased in gastrocnemius (0.8 fold, p < 0.05) and soleus (0.9 fold, p < 0.05) muscles with MI, but increased in soleus (1.1 fold, p < 0.05) muscles with HI. This result is consistent with the change of protein level, suggesting that autophagy might be modulated by different type of exercise. This study suggests that intensity of exercise and different type of muscle fibers effect autophagy gene expression in skeletal muscle of wistar rats. MI exercise increases autophagy gene expression in gastrocnemius and soleus muscles, but HI exercise decreases autophagy gene expression in soleus muscles of wistar rats. Soleus muscles are more responsive to exercise compared to gastrocnemius muscles.