Aim To test whether a geologically recent region with low endemism shows low genetic diversity in a freshwater fish species complex, in contrast to an adjacent area with high diversity. The low endemism is generally postulated to be the combined effect of Pleistocene glaciations and the unstable nature of the recent gravel outwash from young mountains to the west. This rock aggradation has formed a plain, crossed by several braided rivers. The faunas of these rivers have the potential to interchange through flooding or course changes. Location Southern and central South Island, New Zealand (NZ). We define the boundary of these two biogeographical regions as the Waitaki River, the most southerly braided river. To the north lies the Canterbury Plain, formed from coalesced alluvial fans; to the south is the Otago peneplain and associated mountain ranges. Methods Previous work has revealed considerable genetic structuring in the stream-resident fish Galaxias vulgaris Stokell sensu lato, including a species complex in the southern region of South Island, NZ. Using isozyme electrophoresis, we have now examined genetic variation among a total of 58 samples of non-migratory river galaxias from 24 river systems in South Island: 16 in the central region and eight to the south. Results Whereas samples from the central region do exhibit significant genetic structuring (Wright’s FST=0.331), they are more genetically homogeneous (mean Nei’s D= 0.032) than populations to the south of the Waitaki River (FST=0.826, mean D=0.374). Main conclusions The results concur with our expectations of differences between the central and southern regions. We suggest that the divergence in the south reflects geological stability, whereas relatively shallow divergences within the central region reflects the more recent formation of the Canterbury Plain and its unstable braided rivers. The genetic structuring of this group has been promoted by the absence of the marine juvenile phase that is found in five other members of the genus native to NZ. This diversity of the southern region mirrors its diverse flora and invertebrate fauna, and has conservation implications that parallel those resulting from our improved knowledge of the NZ herpetofauna through the application of genetic analysis.