The rate of biodiversity loss across the globe is alarming, suggesting a need to better understand the conditions favourable for generating biodiversity, especially in hyperdiverse regions. The shallow waters of the Indo-Pacific contain the highest concentration of tropical marine species on the planet; not surprisingly, the region has been the focus of extensive study by biogeographers since the 19th century. The Indian and Pacific Oceans border over 65 nations, of which 18 are classified by the UN as Least Developed Countries, with burgeoning human populations along their coastlines.These pressures make understanding the patterns and processes underlying the generation and maintenance of all levels of biodiversity a pressing need.Compared to species diversity, genetic diversity is rarely considered in conservation planning.Genetic diversity data are commonly published as studies of a single or few species, particularly phylogeographic or population genetic studies focusing on spatial patterns within species. Once published, however, these public data can be used to answer questions on a larger spatial scale than the scale of their constituent parts. In a quantitative, comparative framework, these data can be synthesised to address questions about the bewildering diversity of the Indo-Pacific by treating species as 'replicates'. Yet, use of these data carries certain caveats. In particular, data extraction requires significant time and often returns summary statistics rather than raw genetic data. This thesis explores the availability of such data for tropical marine fauna in the Indo-Pacific and makes use of it to examine patterns of genetic diversity at an oceanic scale.The first two chapters of this thesis use publicly available data from 108 studies for 116 species of marine fauna in the tropical Indo-Pacific. In Chapter 2, I discuss the extent and scope of currently published genetic data for Indo-Pacific marine fauna, highlighting its strengths and omissions.I show that there is a distinct bias towards studies reporting genetic diversity for marine fishes compared to marine invertebrates; that most studies focus on a single species and that there is little coherence across regions in terms of species studied. I find that, generally, regions are not consistently co-sampled with neighbouring regions. For example, the same species is not often sampled from the Great Barrier Reef as well as from Indonesia, immediately to the North. I identify locations from where a disproportionately high number of species have been the focus of genetic studies, which may serve as useful 'anchor' locations for researchers to build a network of sampling locations. In an appropriate collaborative framework this could allow the linking of data across very broad spatial extents to explore commonalities across multiple species.The pattern of decreasing species richness of tropical marine taxa with distance from the Coral Triangle is well known. A concordant pattern has been suggested for genetic diversity, however this con...