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This thesis examines cophylogenetic relationships between penguins (Sphenisciformes) and their chewing lice (Insecta: Phthiraptera: Ischnocera). Penguins are parasitised by 15 species of lice in two genera, Austrogoniodes and Nesiotinus. Cophylogenetic studies require robust alpha phylogenies for the groups studied. A new louse species parasitizing yellow eyed penguins, Megadyptes antipodes, is described and new host records for Austrogoniodes demersus parasitising Galapagos penguins, Spheniscus mendiculus, and A. bifasciatus parasitising Humboldt penguins, S. humboldti, are reported. Additionally the taxonomy of little blue penguins, Eudyptula minor, is examined. The taxonomy of little blue penguins has been revised several times and although currently classified as a single species, many authors believe the population breeding around the coasts of Canterbury, New Zealand, to be a distinct species, the white flippered penguin, Eudyptula albosignata. However, little support was found from three gene mitochondrial gene regions (the third domain of the mitochondrial 12S ribosomal RNA gene, cytochrome b and the control region) for the distinctiveness of the white-flippered penguin. The taxonomy of the chewing lice of penguins has been revised several times. Phylogenies for the lice, estimated from 46 parsimony informative morphological characters and molecular data from the third domain of the mitochondrial 12S rRNA gene and a portion of the cytochrome oxidase c subunit I mitochondrial gene using parsimony and maximum likelihood analyses supported the current classification of the penguin chewing lice. No support was found from the phylogenetic analyses for the genus Cesareus that previously contained some species of penguin chewing lice but is currently considered a junior synonym of Austrogoniodes. The term inertia has been used to describe the presence of a louse on several host species. This thesis examines inertia and discusses situations that may result in the occurrence of a parasite species on several host species. The difficulties the presence of widespread parasite species present for cophylogenetic studies are discussed and it is noted that population level genetic techniques may be required to fully analyse some aspects of cophylogenetic relationships. The phylogenies estimated for the lice were compared with a penguin phylogeny estimated from four mitochondrial gene regions. Genetic distances were used to evaluate support for the various cophylogenetic events postulated from a Treemap analysis. Genetic distances suggested the most likely scenario implied six cospeciation events, six duplication events, 11 sorting events, one complete host switch and one incomplete host switch. The cophylogenetic events that have generated the current distribution of populations of three louse morpho-species (A. keleri, A. hamiltoni and A. macquariensis) were unclear, but their distribution is possibly due to inertia (parasites not speciating in response to their hosts speciating). Although the penguin and louse phylogenies were not perfectly congruent it was not necessary to invoke widespread host switching to reconcile the penguin and louse phylogenies.