Aim: Historical connectivity between drainages may represent an underappreciated contributor to the biodiversity within a catchment. First, we tested whether an isolated population of freshwater-limited galaxiids represents a contribution by past interdrainage connectivity to this system’s biodiversity, rather than reflecting intracatchment dispersal or speciation. Second, we sought to distinguish between possible geomorphic processes that could have allowed any past connectivity. Location: The Clutha and adjacent Southland region drainages on the South Island of New Zealand. Methods: We estimated the phylogeographical relationships among 466 cytochrome b sequences from ‘roundhead’ Galaxias populations throughout the Southland region and the Clutha drainage, using three different methods. Subsequently, possible geomorphic mechanisms of interdrainage connectivity were examined concurrently with genetic population divergence time estimates obtained by coalescent analysis. Results: All samples obtained in the lower Clutha system were genetically attributable to G. gollumoides and reflected at least a third, independent colonization event from Southland involving this species, rather than intradrainage dispersal or speciation by pre-existing Clutha populations. Geomorphological inferences and divergence time estimates of less than 7 ka are consistent with headwater connections across low divides between the lower Clutha and the Catlins region of Southland, rather than anastomosing of main channels during low sea stands. Main conclusions: The observation of at least three interdrainage connectivity events influencing the diversity and distribution of G. gollumoides lineages within the Clutha system highlights the potential significance of these processes as contributors to the magnitude and distribution of biodiversity within catchments.