Various models have been proposed to explain the genetic structure of organisms in dendritic stream systems. The headwater and discrete population models describe patterns of genetic structure in organisms who's biological requirements limit their distribution to headwater sections of freshwater systems. The models predict little or no gene flow between populations as the norm, but with enhanced opportunities for crossing drainage divides by living close to upland divides geographically and with specific adaptations for dispersal and persistence biologically; so patterns can be predictably chaotic. The Exquisite Rainbowfish is unique in being one of the few widespread headwater specialist fishes occurring in northern Australia. It is restricted primarily to upland sandstone escarpment habitats in the Kakadu region of the Northern Territory and other small sandstone outcrops stretching into the Kimberley Western Australia. These sandstone escarpment areas are effectively ancient islands of distinct habitat, and are heavily divided by separate drainage systems (e.g. the Kakadu / Arnhem Land Escarpment drains several major river systems including the Daly, Mary, Alligator, Liverpool and Roper). We undertook a study to firstly better map the range of the Exquisite Rainbowfish working closely with Aboriginal ranger groups and land managers. We then undertook a molecular assessment to investigate the broad genetic structure in the species using bi-parentally inherited multi-locus nuclear markers, with a specific focus on taxonomic and evolutionary significant units to inform conservation and management. The results conform to model predications, flagging long isolation for habitat islands and most drainages (cryptic species and major genetic sub-structure) with some selective connectivity across drainage divides in the Kakadu region. Future work will focus on taxonomic descriptions and on highlighting the value of the Exquisite Rainbowfish complex as an aquatic indicator for managing sandstone escarpment habitats.