The aim of this thesis is to use phylogenetic analyses of mitochondrial DNA to investigate the biogeography and evolutionary relationships within the freshwater shrimp family Atyidae in Australia at a nested series of scales, both geographic and systematic. At the largest scale, the relationships between Australian and Indo-West Pacific species were inferred using the two most common atyid genera in Australia, Caridina and Paratya. Most atyids are hypothesised to have colonised Australia from Southeast Asia, but Paratya may be a Gondwanan relict given its distribution. Australian Paratya all form a strong clade, with a sister relationship to species from Tasman Sea islands. Molecular clock estimates place all of the splits within Paratya after the break-up of Gondwana, with Australia being colonised once 3½-8½ million years ago. This transoceanic dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya. Caridina has a very different biogeographic history in Australia, as numerous Australian species have close evolutionary relationships with non-Australian taxa from locations throughout the region. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater taxa, and implies a vicariant explanation due to the development of colder, dryer climates. The systematic relationships of the remaining two Australian surface genera (Caridinides, Australatya) and two subterranean genera (Parisia, Pycnisia) were also investigated. Australatya forms a strong clade with Pacific 'Atya-like' genera, and Caridinides falls within a clade containing Australian Caridina. The hypogean genera, Parisia and Pycnisia, form a strong clade in all analyses, implying an Australian subterranean speciation. The possibility of a relationship between Parisia/Pycnisia and some Australian Caridina species may have implications for the monophyly of the highly disjunct genus Parisia, as it may descend from local Caridina species and represent convergent morphologies. The common and speciose genus Caridina was used as a model taxon for analyses within Australia. At the medium scale, molecular taxonomic techniques were used to uncover cryptic species within a problematic east Australian species complex. At least five species were detected. Phylogeographic and population genetic analyses were carried out on each of these five cryptic species, which diverged from each other in the late Miocene/Pliocene. There were very large differences between the species in the scales of overall geographic distribution, intraspecific divergence and population structure. These were characterised as either: 1) species with large ranges, low intraspecific divergence, limited phylogeographic structuring (Caridina sp. D); 2) species with large ranges, high intraspecific divergence, a high level of phylogeographic structuring (sp. B); 3) species with a limited range, low intraspecific divergence, no phylogeographic structuring (sp. E); or 4) species with limited ranges, high intraspecific divergences, a high level of phylogeographic structuring (sp. A & C). These patterns reflect a combination of large-scale factors, such as landscape structure and climate change, and small-scale factors, such as species-specific tolerances to local conditions and differing dispersal capabilities. Life history variation (egg size) between species may be correlated with different dispersal abilities. Species with the smallest eggs have the least intraspecific divergence and largest distribution, while those with the biggest eggs have the most divergence and smallest distribution, with medium-sized egg species in between. At the smallest phylogeographic scale, C. sp. C from the sand dune islands of Moreton Bay in southeastern Queensland was further analysed. Two different lineages (C1, C2) were found which diverged from each other during the late Miocene/Pliocene and so are older than the current landscape in which they are found. Small-scale phylogeographic analyses within C1, C2 and a sympatric fish identified divergences dating to the Pleistocene (about 100-300 thousand years ago). This implies that ice age sea-level changes may have structured these populations, although there is little observable influence of the last glacial maximum (about 18 thousand years ago). This study has highlighted a number of taxonomic anomalies within the Atyidae. The detection of many cryptic species implies that biodiversity within freshwater invertebrates is higher than currently appreciated. The evolutionary and biogeographic relationships of Australian atyids have proved complex, with many taxa having their own individual histories. At the large Indo-Pacific scale, dispersal is most evident, but within Australia, both vicariance and dispersal have been responsible for structuring all taxa at every scale.