This thesis describes an investigation of the origin, genetic diversity and taxonomy of Didymosphenia geminata, in New Zealand. D. geminata, commonly known as Didymo or Rock Snot , is a freshwater diatom, a photosynthetic alga with a silica shell. It attaches to rocks and plants by its mucilaginous stalks, its large blooms often covering all available substrates and causing shifts in community structure. Although it was historically associated with high altitude, oligotrophic waters, it is now showing increased ecological tolerance. It has been increasing in abundance and range in Europe and North America and has been introduced into new areas including New Zealand, Iran and India. Since the first discovery of D. geminata in New Zealand in October 2004, it has spread rapidly across the South Island. I have conducted a phylogeographic study of D. geminata samples from Europe, Asia, North America and New Zealand, using D. geminata-specific primers to amplify the internal transcribed spacer (ITS) region. I have also used these primers to amplify the small nuclear ribosomal DNA (nrDNA) subunit 18S to investigate the taxonomic placement of D. geminata within the pennate diatoms. Results from this investigation indicate that D. geminata may belong to the Family Cymbellaceae. It appears that D. geminata may have been introduced though several different introduction events to North America from Europe and then to New Zealand from North America. These results can be used to inform strategies regarding the control and management of this invasive species, including lending support for continuation of the Biosecurity New Zealand program aimed at improving public, and especially freshwater users', awareness and responsibility regarding D. geminata in New Zealand. This program is especially important as dispersal appears to be human-mediated. Limiting the number and source of introductions to an area can reduce the potential for increased genetic variation and thus adaptation to new environments.