Our understanding of the diversity and evolution of many marine invertebrates is lacking, especially in the mega-diverse Mollusca. Molecular tools now provide a wealth of approaches for exploring evolutionary patterns. In this thesis I generate mitochondrial and exon capture-based nuclear phylogenies of lndo-Pacific Chromodoris nudibranchs, presenting novel evidence of mimicry and introgression and uncovering eighteen new species. I also conduct cophylogenetic analyses to demonstrate that non-cospeciation events are of central importance in driving the coevolution of endoparasitic gastropods and their echinoderm hosts in Antarctica. Lastly, I erect a new family of truncatelloidean microgastropod using novel morphological and molecular data.