New Zealand is an isolated island nation and more than 95% of its commodities are imported by ship, making New Zealand particularly vulnerable to marine bioinvasion. Its marine biota and ecosystem are unique with numerous endemic organisms, and it is a biodiversity hotspot of global significance. The objective of this study was to integrate invasive theory with phylogeographic studies on a native ascidian. This study was motivated by the introduction of an invasive ascidian, Styela clava to New Zealand. To date, S. clava’s cytochrome oxidase I (COI) data indicate limited sharing of haplotypes between the ports of Lyttelton and Auckland, and areas within Hauraki Gulf. The connectivity between these disparate sites may be a consequence either of common overseas origins via international shipping or local vectoring within New Zealand by coastal shipping. In this thesis I have examined the phylogeographic relationships among populations of an endemic ascidian, Cnemidocarpa nisiotis, to attempt to gauge the likely role that local vectoring plays in the movement of ascidians and other species among New Zealand ports. This study also provides the first population genetic information on a native New Zealand ascidian An endemic New Zealand ascidian was chosen as the study species because the use of an endemic species excludes or at least reduces the possibility of external input from overseas sites con-founding any patterns observed in the data. Furthermore, by excluding external input, the pattern of genetic diversity observed in this species might enable us to determine if local shipping pathways are homogenising C. nisiotis populations. C. nisiotis individuals were collected inside and outside of ports and marinas around Haruaki Gulf, Wellington, Lyttelton, and Dunedin harbours. Each individual were dissected and morphologically identified. Morphological identification of C. nisiotis matched type specimen (Chapter 2). However, preliminary results with COI haplotype network revealed three lineages (A, B and C) and such was the level of differences among these lineages raised the question of the possibility of a cryptic species. This 3 hypothesis was further investigated with phylogenetic analysis using both COI and 18S ribosomal DNA sequence data. Phylogeographic analysis of C. nisiotis COI molecular data demonstrated no significant population genetic structure, with a single common haplotype shared between the North and South islands (Chapter 4). Sharing of haplotypes was also evident between harbours in the South Island and within sites where population samples from inside ports, marinas, and natural habitats were not significantly different from each other. The lack of difference between the North and South Island for this species was surprising given that it was believed to have limited dispersal ability in the absence of anthropogenic movement. However, C. nisiotis displays a star-like phylogeny indicative of a selective sweep, population bottleneck or founder event followed by a population range expansion, thus the lack of difference between islands may be a consequence of too little evolutionary time having passed since the populations shared a common origin for differentiation to have occurred.