Although skeletal and muscle anatomy has supported Gymnuridae as the sister group of the most derived myliobatoids, recent studies based on molecular characters suggest that the family branches into a more basal position than previously thought. This study aims to understand the brain anatomy of the genus Gymnura and its importance in the evolution of the batoid brain. The brain anatomy of Gymnura lessae and Gymnura marmorata is relatively simple. They exhibit a small brain and telencephalon (T), where the latter is wider than it is longer, and the division of the posterior central nucleus is poorly developed. The cerebellum (C) is symmetrical and is not highly foliated. Unlike other species, the brain auricles are smooth, and the posterior auricles exhibit a diagonal arrangement, not always forming a bridge over the fourth ventricle. These auricles are larger in G. marmorata. A principal component analysis based on 20 morphological variables, revealed a separation between species, and multivariate analysis of variance identified significant differences. The most important variables in species segregation were a deeper olfactory bulb in G. lessae and a greater distance between the bulbs in G. marmorata. Contrary to the body anatomy, the brain anatomy reveals that Gymnura has a simpler and more primitive brain than most derived myliobatoids. Our results are consistent with the evidence from phylogenies developed with molecular data, where gymnurids are a basal group within myliobatoids.