The identification of large numbers of single nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions potentially under selection in natural populations. To this end, population genomic approaches that harnesses the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represents a boon not only to test recently developed hypotheses but also to address long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats spanning the Atlantic and Pacific coasts of North America, and portions of England.