In this thesis I investigate patterns of sequence variation at the COI gene in Canadian marine molluscs. The research presented begins the construction of a DNA barcode reference library for this phylum, presenting records for nearly 25% of the Canadian fauna. This work confirms that the COI gene region is an effective tool for delineating species of marine molluscs and for revealing overlooked species. This study also discovered a link between GC content and sequence divergence between congeneric species. I also provide a detailed analysis of population structure in two bivalves with similar larval development and dispersal potential, exploring how Canada’s extensive glacial history has shaped genetic structure. Both bivalve species show evidence for cryptic taxa and particularly high genetic diversity in populations from the northeast Pacific. These results have implications for the utility of DNA barcoding both for documenting biodiversity and broadening our understanding of biogeographic patterns in Holarctic species.