Cladobranchia is a diverse clade of nudibranch gastropods, with ∼1,000 coastal (benthic) and off shore (pelagic) marine species. Their diversity may be tied to dietary specialization and the evolution of remarkable adaptations that are rare among animals, such as the sequestration of cnidarian nematocysts. Due to the deep divergences within Cladobranchia, and other higher-order taxa within Mollusca, phylogenetic analyses based on morphology or a few genes have been unable to resolve relationships within these clades with high support. The introduction of high-throughput sequencing technologies, however, has provided the opportunity to collect large genomic data sets, which have proven useful in resolving relationships within molluscs, as in other metazoan groups. As sequencing costs decrease, it has become easier to collect ever larger data sets in an attempt to resolve relationships within more recently diverged groups, such as Cladobranchia. The phyly and relationships of the three main groups within Cladobranchia (Arminida, Dendronotida, and Aeolidida) have been difficult to determine, primarily due to the rapid evolution of mtDNA and rDNA genes analyzed in traditional molecular phylogenetic studies. In this review, I discuss the systematics of Cladobranchia in regards to morphological data, molecular analyses with one or a few genes, and address the impact of genomic data. I then contend that the supported phylogenetic hypotheses provided by high-throughput sequencing data will provide a better framework for studying taxonomy and character evolution within Cladobranchia, as these data provide strong support for Cladobranchia itself, as well as the nested subclades within it. Although it is important to note that a broader taxon sampling is still needed for genomic data, it is clear that utilizing these data has provided the most-well-supported phylogenetic hypotheses of Cladobranchia to date. In doing so, these genomic data have challenged well-established relationships, including the monophyly of Facelinidae and inclusion of Tritoniidae in Dendronotida, and resolved the position of taxa that have been traditionally quite difficult to place, including Melibe Rang, 1829 and the families Proctonotidae and Dironidae. Finally, these genomic data provide a much stronger phylogenetic framework for studying character evolution within Cladobranchia, including the evolution of nematocyst sequestration, one of the quintessential characters in this clade.