Morphological and genetic analyses of populations of two non-diadromous galaxiid species, the black mudfish Neochnna diversus and the dwarf inanga Galaxias gracilis confirm the presence of a cryptic species, Neochanna heleios, within the geographic range of N. diversus, and indicate three distinct evolutionarily significant units (ESUs) in the latter species. Comparisons between G. gracilis and its parent taxon, G. maculatus, reveal that the former is not monophytetic and derives from three separate founding events. Significant morphological divergence between these two species is the result of ontogenic shifts in landlocked lacustrine populations and long-term morphological convergence in populations of G. gracilis. Corresponding incipient changes are recognized in other younger landlocked populations of G. maculatus in New Zealand. These populations and the three groups within G. gracilis should be given the status of ESUs and managed accordingly by conservation agencies.