At present, there is a general lack of information regarding the spatial genetic architecture and genetic diversity of estuarine and coastal freshwater fish in Australia or about the interacting intrinsic, extrinsic and historical influences responsible for sculpting these patterns. This thesis represented the first investigation of the phylogeographic structure and recent evolutionary histories of teleost fishes from the coastal and estuarine environments of south-western Australia, using the resolution afforded by mtDNA sequence data. Available evidence indicated that, to different degrees, these species have limited potential for dispersal amongst local assemblages from different water bodies. As this theoretically reduces the confounding effects of recent gene flow on extant genetic structure, these fishes were well suited to studying the influences of historical factors. Historical influences were expected to be particularly profound, given that these coastal environments underwent massive modifications during Late Quaternary eustatic fluctuations. The thesis consists of four major components, which explored different aspects of interspecific and intraspecific phylogeny and p hylogeograp hy of three teleost species, based on mtDNA control region and cytochrome b fragments. First, the relationship between the endemic, 'strictly estuarine' Leptatherina wallacei (Atherinidae) and the more widespread, 'estuarine & marine' 6. presbyteroides was examined, with a view to establishing whether 6. wallacei represents a monophyletic or polyphyletic lineage and whether this species was derived recently (i.e. in Holocene estuaries). Second, the phylogeographic structure and genetic diversity of L. wallacei were investigated and compared with data from L. presbyteroides, with a view to using this information to interpret the recent evolutionary histories of each congener. Third, the divergence between assemblages of L. wallacei inhabiting two isolated coastal lakes was used to estimate a maximal substitution rate for the control region, which was then used to infer general time frames for the divergence between the two Leptatherina species and between the major phylogeographic partitions within each species. Fourth, investigations were initiated into phylogeographic patterns and levels of genetic diversity within and among assemblages of Pseudogobius olorum (Gobiidae) from several coastal lakes and an estuary. Phylogenetic analyses indicated that the two Leptatherina species were characterised by exclusive and reciprocally-monophyletic lineages of haplotypes from both mtDNA regions, supporting the monophyletic origins of L. wallacei. Both 6. wallacei and 6. presbyteroides exhibited high levels of genetic diversity and extensive overall subdivision (e.g. Qsr = 0.691 & 0.644 respectively for control region data). There was a profound phylogeographic break in both species between all conspecific assemblages from the lower west coast (LWC phylogroup) and all those from the south coast (SC phylogroup), which suggested the influences of shared extrinsic and/or historical factors. There was limited genetic structuring within the two major phylogroups of either Leptatherina species, apparently reflecting recent connectivity amongst local assemblages, with subsequent fragmentation and insufficient time for lineage sorting. However, two major phylogeographic breaks distinguished monophyletic control region phylogroups of L. wallacei from the isolated coastal Lake Clifton and Lake Walyungup, consistent with their independent evolution following lacustrine entrapment during the Holocene. The divergence between these two isolated lacustrine assemblages of Leptatherina wallaceiformed the basis for an estimate of the maximal substitution rate of the control region. While these data were unable to provide a precise estimate of the actual rate of molecular evolution, all the evidence suggested that it was proceeding very rapidly. The maximal rate estimate of 172.3% lineage-' MY-' was among the fastest ever reported. Based on this rate, the two Leptatherina species diverged at least 1 SKya, thus rejecting a Holocene origin for L. wallacei. The divergence between the LWC and SC phylogroups of L. wallacei has been ongoing for at least GKya, while the equivalent divergence in L. presbyteroides has been ongoing for at least 11 Kya. As the time frames of these divergences were consistent with periods of massive environmental modifications associated with the end-Pleistocene fall in sea level and the HMT, it was likely that these factors have played important roles in sculpting the species' divergence and intra-specific genetic structure. Although useful in temporally scaling genetic divergences within and between the two Leptatherina species, wider application of this rate estimate to questions regarding other taxa was limited. For example, evident rate heterogeneity between the genera precluded its use with even the relatively closely-related atherinid Atherinosoma elongafa. Phylogeographic analyses identified high levels of genetic diversity and extensive genetic subdivision (e.g. st = 0.652 for control region) amongst an estuarine and several lacustrine assemblages of Pseudogobius olorum, although phylogeographic structure was shallower than in either Leptatherina species. There was increased divergence between three assemblages from the lower west coast and two from the south coast, consistent with the profound break evident in the Leptatherina. One lacustrine assemblage appeared to represent a distinct lineage and a preliminary maximal rate estimate (~61.4% lineage-1 MY-1) was calculated based on the minimum divergence of this assemblage from its nearest conspecifics. Although slower than the rate calculated for L. wallacei, this was still high for teleost fishes. Overall, this study indicated that historical environmental factors, especially those related to Quaternary eustatic changes, have played important roles in sculpting the phylogeography and evolution of three teleost species from south-western Australia. Moreover, as these species have differential dependencies on estuarine environments (is. 'strictly estuarine' vs 'estuarine & marine') and represented two different taxonomic groups (i.e. Atherinoidei & Gobioidei), historical environmental factors may have exerted similar influences on other coastal species in the region.