Vertebrates consist of two main phylogenetic groups: jawed vertebrates, or gnathostomes, and cyclostomes, extant agnathans. Therefore, comparisons between gnathostomes and cyclostomes are essential to infer the condition of the last common ancestor of vertebrates. The hagfish, together with the lamprey, represents one of the two lineages of cyclostomes. Most genomics resources of cyclostomes come from studies with the lamprey, being the resources for hagfish species very limited. We provide here RNA-seq data from 3 different embryos and a juvenile of the Japanese inshore hagfish, Eptatretus burgeri, and from a series of developmental stages of the the Artic lamprey, Lethenteron camtschaticum, and the cloudy catshark, Scyliorhinus torazame, in order to provide a invaluable resource for evolutionary development studies trying to understand the evolution of vertebrates.