The aim of this study was to compare the effects of two training protocols, training on alternate days (A) or on consecutive four days followed by three days of rest in each week (C) for eight weeks, on selected proteins involved in the biogenesis and function of mitochondria in skeletal muscle. Eighty male SD rats were randomly allocated into 10 groups (n=8 each), including Pre and Post control groups, and A or C training groups with 8, 16, 24 and 32 training sessions, respectively. The vastus lateralis and soleus muscle samples were obtained 24 hours after the last training session, or at rest for the controls. The abundance of the proteins for PGC-1α, CaMKII, NRF-1, mtTFA and COXIV was analysed by Western blotting. Analysis of the results with two-way ANOVA showed no significant effect and interaction (training protocol by duration) in abundance of the proteins by the two protocols. However, fold changes normalized to control showed significant increases COXIV of the soleus muscle at most time points in both A and C training as indicated by Krumkal-Wallis H tests. There were significant correlations found between the abundance of the measured proteins of the vastus lateralis. The findings suggest that the two training protocols with the same intensity and total volume of work would not make a significant difference in respect of the changes in the targeted proteins. Alternative regulatory factors and the responses in different types of muscles to the training programs need to be examined in future research.