Batoids (skates and rays) are the most speciose group of cartilaginous fishes. Their body plan represents diverse ecologies and swimming modes. Early skeletal fossil remains, and recent phylogenetic analyses suggest that convergence has occurred within the batoids several times independently. The drivers for such disparity patterns and possible association with modularity and phenotypic integration among batoids are not fully understood. Here we used geometric morphometrics and phylogenetic comparative methods to characterize the evolutionary trends of the basal fin skeleton of batoids and sharks. Our analyses show that the morphological variation has a strong phylogenetic signal. Interestingly, the most speciose orders of batoids display low morphological disparity. Reef and freshwater species, show increased evolutionary rates. Meanwhile, the swimming mode shows different rates depending on the fin structure analyzed. A higher modularity and integration signal suggest that the pectoral fin of batoids has experienced mosaic evolution. The low morphological disparity might be associated with high integration. We find support for convergence between Jurassic, Cretaceous, and Extant guitarfishes, however, not completely between sharks and batoids. Our findings suggest that habitats and swimming mode have shaped the pectoral fin evolution among batoids, and at the same time batoids have constrained their basal fin skeleton.