Closely related species may have different patterns of distribution and spatial population structure in common landscapes, which can have implications for conservation of the species if they are vulnerable. The Australian mountain galaxias species complex has recently been split into 15 described species, 11 of which are threatened. In this study, we assessed the distribution and landscape genetic structure of two mountain galaxias species (Galaxias olidus and Galaxias oliros) in the Goulburn–Broken catchment (Murray–Darling Basin) in relation to hydrographic descriptors of river terrain, network and hydrology. We also assessed small-scale population structure in juvenile G. oliros in tributary streams of the Goulburn River (the Granite Creeks). Analyses of distribution revealed that G. olidus mostly occurs in smaller streams at high elevations with steep valley slopes and high stream gradients downstream, whereas G. oliros mostly occurs in larger downstream waterways with higher magnitude and variability of stream flow. Population genetic structure in G. olidus was much greater than for G. oliros, with 17 of the 19 sampled locations resolved as genetically distinct populations for G. olidus, but only a single population revealed for G. oliros. Results for both species did not reflect the expectations of the stream hierarchy model or isolation-by-distance model. However, small-scale spatial population structure in juvenile G. oliros in the Granite Creeks reflected the expectations of both stream hierarchy and isolation-by-distance models, suggesting that population structure of juveniles of this species reflects some level of spatial aggregation of closely related individuals that probably diminishes as the population ages. Higher landscape genetic structure in G. olidus was correlated with steeper stream and valley slopes, whereas no population genetic correlations were significant for G. oliros. Genetic diversity in G. olidus was higher in areas of greater hydrological variability, suggesting that populations in hydrologically variable areas function as a metapopulation and have a more diverse gene pool than populations in areas with lower hydrological variability. In contrast, genetic diversity in G. olidus was lower in higher elevation areas with steep valley slopes, suggesting that smaller but more stable populations occur in high elevation streams with high perenniality and low interannual variability of flows. Our results are consistent with other studies that highlight the importance of supporting natural hydrological regimes and natural patterns of hydrological connectivity for conservation of vulnerable freshwater fish.