This magnum opus concerns the generation of genomic level data, through next generation sequencing technologies, and the application of these new molecular libraries to various aspects of protostome evolution. In Chapter 1 I introduce the most important contribution to the field of evolution: Darwin’s Theory of natural selection, the keystone to our current understanding and methodologies. Following this I discuss the first applications of such knowledge to morphological and molecular data, the theory behind the bioinformatics techniques used to analyse such information, and how recent advancements in sequencing technologies have opened the door to large-scale studies of evolution. After these principles are established a summary of the clade of animals that are the focus of this thesis: the Protostomia is provided. Chapter 2 is a study of a remarkably adaptable group of ecdysozoans called the tardigrades or “water bears”. Their rapidly evolving nature has made the phylogenetic affinity of the Tardigrada ambiguous with three alternative hypotheses contesting their placement. A phylogenomic approach was implemented in order to clarify their position in conjunction with signal dissection experiments to minimize systematic error. The origin of the Tardigrada was also investigated using a series of molecular clocks. Important findings from this chapter include evidence that the tardigrade-nematode grouping is a systematic artifact known as long branch attraction, their true affinity lying with the onychophorans, and that the tardigrade lineage diverged some 480 million years ago in the Lower Ordovician period, slightly older than previously thought (Rota-Stabelli et al. 2013). Chapter 3 comprises a detailed study of one of the first animal predators to originate: the Chaetognatha. Molecules and morphology have clashed on its bilaterian affinity and molecular studies remain in wide disagreement as to their exact position with the Protostomia. The newly sequenced Parasagitta sp. genome was incorporated in to a pre-existing ecdysozoan dataset and phylogenomic reconstruction methods and divergence time estimation experiments were implemented to uncover the eventful 520 million year evolutionary history of these ancient carnivores. Results from these experiments show that the chaetognaths are unequivocally protostomes with a deuterostome-like development and that their true placement within this group is as basal lophotrochozoans. Moreover a large discrepancy discovered between the age of the fossil and extant chaetognaths points to an extinction event within the lineage that had previously not been reported. This signifies a remarkable example of an animal that has undergone a complete role reversal in the food chain during its 500 million year reign: from ancient predators to contemporary prey. Chapter 4 describes my involvement in a collaborative work on a palaeobiological exploration of arthropod terrestrialization. New molecular libraries from the Crustacea and Myriapoda were used to investigate the independent colonization events of the arthropod subphyla. Our results from this study support Erwin et al. (2011) and dos Reis et al. (2015) findings of a Cryogenian origination for the Metazoa and a Lower Cambrian radiation of animal lineages. The arachnids were the last of the terrestrial arthropods to colonize land in the Upper Ordovician (450 MYA), with the hexapods colonizing land in the Lower Ordovician (483 MYA) broadly in agreement with the fossil record. However the Myriapods colonized land twice, initially in the Cambrian (543 MYA) and then in the Lower Ordovician (473 MYA). The implications of which suggest that terrestrial ecosystems capable of supporting life existed as far back as the Cambrian time period over 500 MYA. Finally Chapter 5 details the application of phylostratigraphy to a large-scale study of novel protein families spanning the Metazoa with a focus on the Protostomia and Ecdysozoa. Twenty-eight taxa from next generation sequencing experiments contributed to this work and were the subject of homology searches using BLAST and protein family clustering using MCL, which were then distributed across a forty-eight node cladogram ranging from the roots of the Animal Kingdom to the tips of the arthropod subphyla. The rate of protein family acquisition has increased in ancient high-level taxonomic nodes compared to that of the younger nodes and lineages in the tree, suggesting that protein families functioning within extant animals have existed for a considerable amount of time before these animals diverged. The tweaking of these families, more so than the gradual increase in family numbers, has influenced the evolution and diversification of the animal lineages existing today.