Rubredoxin:oxygen oxidoreductase (ROO) is the terminal oxidase of a soluble electron transfer chain found in Desulfovibrio gigas. This protein belongs to the flavodiiron family and was initially described as an oxygen reductase, converting this substrate to water and acting as an oxygen-detoxifying system. However, more recent studies evidenced also the ability for this protein to act as a nitric oxide reductase, suggesting an alternative physiological role. To clarify the apparent bifunctional nature of this protein, we performed molecular dynamics simulations of the protein, in different redox states, together with O(2) and NO molecules in aqueous solution. The two small molecules were parameterized using free-energy calculations of the hydration process. With these simulations we were able to identify specific protein paths that allow the diffusion of both these molecules through the protein towards the catalytic centers. Also, we have tried to characterize the preference of ROO towards the presence of O(2) and/or NO at the active site. By using free-energy simulations, we did not find any significant preference for ROO to accommodate both O(2) and NO. Also, from our molecular dynamics simulations we were able to identify similar diffusion profiles for both O(2) and NO molecules. These two conclusions are in good agreement with previous experimental works stating that ROO is able to catalyze both O(2) and NO.