Background: People with osteoarthritis are at increased risk of cardiovascular diseases. However, regular exercise and ozone therapy can prevent such diseases. Objectives: The current study aimed to investigate the effect of aerobic training and ozone therapy on the gene expression of MFN1 and DRP1 in the heart tissue of rats with osteoarthritis. Methods: In this experimental study, 24 rats with osteoarthritis were randomly divided into four groups of six rats, including (1) osteoarthritis control, (2) training, (3) ozone, and (4) training + ozone. Also, to investigate the effects of osteoarthritis on intended variables, 6 healthy rats were selected as the healthy control group. Then, for the next eight weeks, rats in the aerobic training groups were planned to run on the treadmill five sessions per week for 30 - 50 minutes, and those in the ozone groups received 20 µg/mL ozone once per week for three weeks, 21 days after induction of osteoarthritis. Gene expression levels of MFN1 and DRP1 were measured in the heart tissue. The Shapiro-Wilk, one-way ANOVA, and Tukey’s post-hoc tests were used to analyze the data (P ≥ 0.05). Results: Induction of osteoarthritis was associated with increases in MFN1 (P = 0.001) and DRP1 (P = 0.001). However, in the training, ozone therapy, and training + ozone therapy groups, osteoarthritis decreased the DRP1 (P = 0.001); training (P = 0.02), ozone therapy (P = 0.002), and training + ozone therapy (P = 0.001) decreased the MFN1; Also, reduction in MFN1 and DRP1 was greater in the training + ozone therapy group than the sole training group (P = 0.001). Conclusions: Although eight weeks of training and ozone therapy improved the levels of MFN1 and DRP1 gene expression in the heart tissue of rats with osteoarthritis, simultaneous use of training with ozone therapy showed more favorable effects on the improvement of MFN1 and DRP1 gene expression levels than sole training or ozone therapy alone.