In general, the development of the theory of the legal system has focused on the contributions of legal positivism authors, leaving to one side the contributions of natural law theory. This study seeks to rebuild the theory of the legal system developed by the School of Salamanca's founder, Francisco de Vitoria, showing its explanatory advantages in comparison with the first analytical legal theory of legal system formulated by John Austin. This study shows that, just as in Austin, it is possible in Francisco de Vitoria to reconstruct the existence and identity criteria of legal systems from the notions of command and sovereignty. These findings allow us to maintain that 300 years before Austin, and in a non-analytical environment, Francisco de Vitoria developed a theory of legal system.