Batoids (skates and rays) are the most speciose group of cartilaginous fishes with a diverse array of ecological adaptations and swimming modes. Early skeletal fossil remains and recent phylogenetic analyses suggest that convergence among batoids has occurred independently multiple times. The drivers for such disparity patterns and possible association with modularity and phenotypic integration among batoids are not fully understood. Here we employed geometric morphometrics and phylogenetic comparative methods to characterize the evolutionary trends in the basal fin skeleton of extinct and extant batoids and dorsoventrally flattened sharks. We found that the most speciose orders of batoids, Myliobatiformes and Rajiformes, display the lowest levels of morphological disparity, while Torpediniformes and Rhinopristitiformes have the highest disparity. Differences in evolutionary rates by habitat indicate that both reef and freshwater species evolved faster than deep-sea and shelf-distributed species. We further explored the differences based on swimming modes and found that species with oscillatory swimming exhibit higher evolutionary rates on their coracoid bar. We found that specific groups underwent different rates of evolution on each element of the pectoral fin. This was corroborated by the modularity and integration analyses, which indicate differences in the covariation between structures among the analyzed groups. The convergence analysis does not support the resemblance between flattened sharks and batoids; however we found convergence between extinct batoids and modern guitarfishes. Our findings suggest that habitat and swimming mode have shaped the pectoral fin evolution among batoids.