Cnidarians are an excellent system for studying the evolution of complexity and novelty given their diversity in body plan organization and life history strategy. Building on the advances made possible by the Hydractinia genome sequencing project, we are generating a high-quality genome sequence for the closely related hydrozoan, Podocoryna carnea which, unlike Hydractinia, has a pelagic medusae (jellyfish) phase. These genomic data will significantly advance comparative genomics studies aimed at identifying the genomic toolkit specific to production of the medusa life cycle stage and its constituent cell types, some of which are stage-specific and potentially convergent to bilaterian cell types such as striated muscle and photoreceptor cells. We will also extend our current studies on allorecognition and sex determination in Hydractinia to P. carnea, with a focus on whether possessing a pelagic life cycle stage alters the genetic architecture of these processes. Our initial sequencing of P. carnea laboratory strains reveals that its genome is highly heterozygous, leading us to adopt a trio-binning strategy for assembling a fully phased genome of P. carnea by long-read sequencing of an F1 individual and short-read sequencing of both of its parents. The preliminary Illumina assemblies of the parental genotypes and PacBio assembly of the F1 (N50 > 1.5 Mbp) have already proved useful for identification of medusa-specific genes and potential allorecognition sequences. Ongoing improvements to the P. carnea genome sequence, along with current and planned stage- and tissue-specific single-cell RNA sequencing efforts, will advance the tractability of P. carnea as a model for evolutionary genomics.