The purpose of the present study was to compare the influence of aerobic exercise (AE) lasting 12 weeks to that of resistance exercise (RE) of the same duration on endoplasmic reticulum (ER) stress and mitochondrial biogenesis in the cardiac muscle of middle-aged obese rats. Obesity was induced in thirty 50-week-old male Sprague Dawley rats over 6 weeks by administration of a high-fat diet. The rats were then subjected to treadmill-running (AE) and ladder-climbing (RE) exercises 3 times per week for 12 weeks. Rats in the AE group showed significantly lower increases in body weight and intraperitoneal fat than those in the sedentary control (SC) group (P<0.05). The 12-week exercise regimes resulted in a significant increase in expression of mitochondrial biogenesis markers and levels of peroxisome proliferator-activated receptor gamma coactivator 1α in the cardiac muscle (P<0.05). Phosphorylation of PKR-like ER kinase, an ER stress marker, decreased significantly (P<0.05) after the exercise training. Although a trend for decreased C/EBP homologous protein (CHOP) expression was observed in both exercise groups, only the AE group had a statistically significant decrease (P<0.05). Levels of GRP78, an ER stress marker that protects cardiac muscle, did not significantly differ among the groups. Although only the AE group decreased body weight and fat mass, the two exercise regimes had similar effects on cardiac muscle with the exception of CHOP. Therefore, we suggest that both AE, which results in weight loss, and high-intensity RE, though not accompanied by weight loss, protect obese cardiac muscle effectively.