Members of the oomycete class include some of the most devastating pathogens of plants and animals. Oomycetes secrete large arsenals of effector proteins that perform a wide range of functions, including sequestering nutrients from hosts and the environment, degrading host cells to facilitate colonisation, and modulating host immune responses. Recent genome sequencing projects have generated large amounts of oomycete genomic data. Availability of which facilitated bioinformatic characterisation of the secretomes of diverse oomycete species. Using comparative genomic, network, and phylogenetic methods, this thesis reports the identification of lineage and species-specific expansions of effectors. Despite their ubiquity and the threat that oomycetes pose to global food security, there is a lack of dedicated tools to analyse oomycete genomes. To this end, the Oomycete Gene Order Browser (OGOB) was developed. OGOB is a database and novel tool that facilitates comparative genomic and syntenic analyses of oomycete genomes. Analyses using OGOB highlighted the high degree of syntenic conservation within oomycete genera. Furthermore, tandem gene duplication was shown to play a significant role in the expansion and evolution of effector proteins. The data presented in this thesis also describes the first large-scale genomic and proteomic investigations of the widespread phytopathogens Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae. Mass spectrometry analyses identified approximately 300 extracellular proteins per species, many of which are putativly involved in infection or osmotrophy. The expression of approximately 3,000 proteins for each species was validated at the protein level. Comparative genomic analysis of CAZymes suggest that oomycete lifestyles may be linked to their CAZyme repertoires. Overall, the data presented in this thesis expands our knowledge of oomycete genome evolution.