To truly understand evolution, we must document patterns of variation in traits – ranging from anatomical features of individuals to geographic ranges of species – to gain insights into the mechanisms that lead to changes in diversity through time. This type of work requires a robust historical context of evolutionary relationships in order to make comparisons across taxa and inferences about past events. My dissertation provides a thorough phylogenetic analysis of the marine gastropod group Cladobranchia (Mollusca) to better understand the evolution of defensive capabilities within the clade. In the absence of a protective shell, lineages within Cladobranchia have evolved a diverse array of alternative defense mechanisms, including the use of stinging organelles (nematocysts) acquired from their cnidarian prey. It has been hypothesized that incorporation of nematocysts as a defensive strategy may have been an evolutionarily important event that led to large-scale diversification within this group. As such, understanding the steps involved in the evolution of this ability is necessary for evaluating this hypothesis. A major objective for my dissertation has been to use transcriptome (RNA-Seq) data from 37 species in Cladobranchia in order to generate a well-supported phylogenetic hypothesis of Cladobranchia. This research has produced the most highly supported phylogenetic tree of Cladobranchia thus far and contributes to confidence in the efficacy of genomic data to resolve relationships among gastropod lineages. As I have been able to expand this phylogenetic hypothesis with additional taxon sampling, including molecular data from a further 60 species, I have been able to provide context for understanding the evolutionary steps that led to the ability to sequester nematocysts. This phylogeny was then combined with morphological data from 50 nematocyst sequestering species within Cladobranchia to allow for a more detailed reconstruction of the evolution of nematocyst sequestration and prey preference within this clade. Overall, this work builds knowledge of the relationships among major lineages within Cladobranchia, and has substantially increased understanding of the evolution of morphological and ecological characters in this group.