Invertebrate organisms represent 95% of animal biodiversity, however, few genomic resources currently exist for the group. We focus on marine invertebrates, which include the most ancient animal lineages. Their genomes will provide insight into deep-time evolution as well as carry information about the influence of selection and signatures of (ecological) adaptation. A grand challenge is to extract this information from non-model species, generally not amenable to laboratory conditions, with small body sizes and large and complex genomes.