Cnidarians form the sister group to bilaterians, and are a diverse phylum of animals. While there are many established model organisms within Cnidaria, there are still entire clades of organisms that are not represented in scientific studies due to the difficulty in sampling them or cryptic species and subspecies. Ceriantharia holds a unique position within Cnidaria, as the sister group to the remaining hexacorals according to the most recent phylogenomics analyses. Up to this point, however, the data available for cerianthids has been either transcriptomic, or from a small subset of genes. Here we report the draft genome from a cerianthid species, Cerianthus borealis. We used a combination of long and short-read sequencing technologies to produce a highly contiguous genome assembly that is 492 Mb in length and has a scaffold N50 of 396 kb. This genome will provide a resource to investigate questions about the evolutionary history of unique traits, gene families, and the phylogenomic distribution and ancestral state of mitochondrial genome structure within cnidarians, among others. Additionally, the low-cost rapid sequencing and bioinformatic workflow developed herein will be useful for future studies involving the sequencing, assembly, or annotation of other marine invertebrate genomes.