Ctenophores, also called the comb jellies, are a diverse phylum of gelatinous animals found in most marine areas of the world. The organization of species within the phylum remains poorly resolved, with previous studies making use of only ribosomal RNA as a phylogenetic marker. Here we sequenced transcriptomes of 36 ctenophores across all major groups of the phylum to an average sequencing depth of 4.8 gigabases to assess phylogeny and other important biological traits.