BACKGROUND: Mitochondrial fission and fusion both contribute to maintaining mitochondrial function and optimizing bioenergetic capacity. OBJECTIVE: The aim of this study was to compare the effect of aerobic and resistance training on mitochondrial fission and fusion markers in skeletal and cardiac muscles of Wistar rats. METHOD: 24 male Wistar rats were randomly divided into four groups of moderate-intensity interval training (MIIT), high-intensity interval training (HIIT), resistance training (RT) and control (CON). The MIIT and HIIT groups performed treadmill exercises with an intensity of 60-65% and 80-85% of the maximum speed, respectively, while the RT group performed resistance training with an intensity of 30-60% of the rat's body weight for 8 weeks. The soleus (SOL), extensor digitorum longus (EDL) and left ventricular tissues were used to evaluate markers of mitochondrial fission and fusion PGC-1α (fusion/fission), Opa-1 (fusion), Fis-1 (fission), Drp-1 (fission), Mfn-1 and Mfn-2 (fusion) genes expression. RESULTS: In all three tissues, a significant increase in some mitochondrial fusion markers was observed after 8 weeks of training (p = < 0.0001-0.0452). Furthermore, a significant decrease in cardiac mitochondrial fission markers was observed in all three groups (p = < 0.0001-0.0156). This reduction in some markers was evident in the SOL tissue of the HIIT group (p < 0.0001 for Drp-1 and p = 0.0007 for Fis-1) and in the EDL tissue of the RT group (p = 0.0005 for Fis-1 and p = 0.0012 for Drp-1). The mitochondrial fission/fusion markers in the heart (p = 0.0007-0.0449) and SOL (p = 0.0050-0.0258) tissues of the HIIT group had more changes than the RT group, while the mitochondrial fission markers in the EDL tissue of the RT group had a lower level than the HIIT (p = 0.0087 for Drp-1) and MIIT (p = 0.0130 for Fis-1 and p = 0.0010 for Drp-1) groups. CONCLUSION: Our study demonstrated that HIIT, through better regulation of mitochondrial fusion and fission than RT, improves mitochondrial dynamics in cardiac and SOL tissues.