Phylogeographical studies based on DNA sequences offer insights into intraspecific genetic patterns, elucidating the history and structure of populations and their habitats. We used mitochondrial DNA (cytochrome b) to study the phylogeography and population genetics in two sympatric species in the freshwater fish genus Philypnodon throughout south-eastern Australia. We sought to determine how populations were related across drainage divides, and whether transfer among adjacent coastal drainages was related to continental shelf width or intradrainage distance. Phylogeographical structure was greater in Philypnodon macrostomus Hoese Reader, 2006 compared with Philypnodon grandiceps (Krefft, 1864), with results for P. macrostomus showing evidence for the presence of distinct groupings in different areas of south-eastern Australia. There was evidence of drainage-divide crossings in P. grandiceps in western Victoria, and in P. macrostomus between the Burnett River and the Murray-Darling Basin in south-eastern Queensland. Both species showed low levels of divergence along the narrow continental shelf of New South Wales, but as continental shelf width increased moving north in south-eastern Queensland, population divergence also generally increased. Thus, as the potential riverine connectivity during periods of low sea levels increased, genetic divergences also increased, counter to expectations. Also, population Fst measures did not correlate as predicted with continental shelf width, nor was a significant relationship detected between Fst and the distance between populations.