Manta rays and their relatives of the family Myliobatidae have pectoral fins that have been modified for underwater flight, as well as a pair of fleshy projections at the anterior of the body called cephalic lobes, which are specialized for feeding. As a unique trait with a dedicated function, cephalic lobes offer an excellent opportunity to elucidate the processes by which diverse body plans and features evolve. To shed light on the genetic underpinnings of cephalic lobes, we examined various domains during paired fin development in cownose rays (Rhinoptera bonasus), which represent the sister taxon to manta rays in the genus Mobula, using RNA-Sequencing and comparative transcriptomics. By comparing gene expression patterns to publicly available data from the little skate (Leucoraja erinacea), our data illustrate how distinct body plans and seemingly novel features can arise via subtle changes to existing developmental pathways.