Oomycetes are ubiquitous fungus-like protists which include serious pathogens of agricultural, horticultural, and aquatic commodities. Proper identification to the species level is a critical first step in any investigation of oomycetes, and the use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase (COI) is a relatively new and potentially useful approach that had yet to be assessed over a significant sample of oomycete genera. DNA sequencing of COI from 1205 isolates representing 23 genera and a comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI-based identification and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources. Due to the fact that studies o f oomycete evolution and taxonomy have traditionally been heavily reliant on ribosomal RNA and mitochondrial cytochrome oxidase sequencing to infer species boundaries and higher level phylogenetic relationships, a new approach to oomycete molecular systematics was undertaken using two single-copy protein-coding flagellar genes, PF16 and OCM1, showing their utility in species delimitation and in phylogenetic reconstruction o f oomycete evolution. This approach also demonstrates, a recently proposed codon substitution-based phylogenetic method. Using the codon model, the phylogenetic relationships inferred by flagellar genes are largely in agreement with the current views of oomycete evolution, whereas nucleotide and amino acid models failed to reconstruct monophyly in several clades. Interesting parallels exist between the molecular evolution of flagellar genes and zoospore ontology, supporting the tree obtained using the codon model. Sequencing of OCM 1 in particular revealed high variability among oomycetes and indicated a potential role of this protein in host-interaction of zoospores. A hypothesized role of OCM1 in host recognition, possibly through interaction with host C-type lectin was tested, and although the role of OCM1 was not confirmed, plant C-type lectin was shown to contribute to susceptibility of Arabidopsis seedlings to Pythium zoospores. This is a novel and important finding which helps to understand the unknown function of C-type lectin in plants. As a whole, this thesis contributes new resources and knowledge to the study of oomycetes, molecular evolution, and plant pathology.