Non-bilaterian phyla represent key lineages for exploring the evolutionary history of early animals. However, despite an increasing number of sequenced genomes from early-branching metazoans, efficient and reproducible methodologies for analysis of gene function remain a major challenge. Here we report the utilization of the TALEN and CRISPR/Cas9 systems to induce targeted mutations and homologous recombination-mediated transgenesis in the sea anemone Nematostella vectensis. We also present a new method to isolate genetically modified animals using engineered selection cassettes introduced by homologous recombination. Taken together, these methods will permit sophisticated gain- and loss-of-function analyses in Nematostella and perhaps other early metazoan species that allow for zygotic injection.