Access to a growing number of marine invertebrates with genetic and genomic tools has broadened our understanding of the diversity of developmental mechanisms, informing our understanding of larval evolution by allowing the identification of shared or divergent programs for the formation of body plan patterning and organ formation. Two such genetic programs are the apical plate patterning network and the hox/parahox trunk and gut patterning network common to larval and adult forms, respectively. While mounting evidence supports an ancient origin at the base of the Bilateria for both adult and larval forms, it is clear that many distinct organs and structures have appeared independently and can be shifted between the larval and adult phase frequently. Future advances in our understanding of larval evolution are likely to emerge from exhaustive studies of marine invertebrate cell types by single-cell sequencing technologies and through the study of the genetic basis of the metamorphic transition.