Abstract
Many of New Zealand's Galaxias species have declined in abundance this century. Some stream‐resident species are now restricted to sections of tributaries above waterfalls >3 m in height that act as barriers to the predatory brown trout (Salnto trutta). It has been suggested that these spatially isolated populations are also genetically isolated and as a result experience restricted gene flow. We used isozyme electrophoresis to test this hypothesis. Comparisons were made between and within tributaries at sites separated by waterfalls. Results from six polymorphic loci showed evidence of genetic heterogeneity among populations of G. anomalus and G. depressiceps from tributaries of the Taieri River system, South Island, New Zealand. In one instance, heterogeneity was found within a single tributary. This demonstrates that gene flow among populations is restricted and that waterfalls are likely to be a significant influence in controlling galaxiid population structure.