This thesis aims to initially define the present knowledge of pathogens which infect algae, highlighting the potential economic significance of such pathogens, given the recent rise in algaculture. Focus is given to the oomycetes, a group of organisms which already contain several significant genera of plant (Phytophthora) and animal (Saprolegnia) pathogens, as well as Olpidiopsis; a genus reported to significantly impact algaculture in Asia. Subsequent chapters aim to genetically characterise stramenopiles (specifically oomycetes and hyphochytrids) associated with algae in two ways. Firstly known pathogens of algae, Olpidiopsis feldmanni and Anisolpidium rosenvingei are morphologically diagnosed by microscopy and genetically surveyed at phylogenetically significant loci. Further morphological information on these two pathogens is reported here expanding the current knowledge of these rarely reported organisms. Surprisingly, genetic evidence indicates that Anisolpidium, a uniflagellate genus, belongs to the biflagellate class Oomycota and not the closely related uniflagellate class Hyphochytriomycota, as previously suspected. Morphological and genetic features of these classes are contrasted to justify this molecular interpretation. These first two studies, along with the publically available sequences of algal pathogens are then used to design primers, which enable an oomycete-directed metagenomic survey of brown algae, allowing the investigation of what organisms are associated with these. At present the results of this survey are unreported. Finally a Eurychasma dicksonii transcriptome as well as genomic sequences of other stramenopiles are investigated for the presence of cadherin protein models. At present such models are automatically annotated and reported. This study is the first manual curation of the protein and defines a unique protein family which is presented by the oomycete genera Eurychasma, Pythium, Phytophthora and Albugo as well as the labyrinthulomycete Aurantiochytrium limanicum. The protein model is not reported from other sequenced oomycete genera or photosynthetic stramenopiles.