The Atherton Tablelands region in Queensland is home to exceptional rainbowfish species diversity, including the Endangered Lake Eacham rainbowfish (Melanotaenia eachamensis) and the Critically Endangered but undescribed Malanda rainbowfish. These species are known from only a small number of populations and are threatened by the risk of hybridisation with the widespread eastern rainbowfish (Melanotaenia splendida). Understanding the genetic history of these populations is therefore critical to understanding their evolutionary history, accurately delineating species boundaries, and implementing appropriate conservation management. We develop species networks - which allow for both population splits and gene flow between populations - to examine the evolutionary history of Tablelands rainbowfishes. We reveal multiple instances of gene flow between M. splendida and populations of both M. eachamensis and Malanda rainbowfish. We also find gene flow between Malanda rainbowfish and the now-extinct population of M. eachamensis in Lake Eacham, the type locality of this species. These results have important implications for species delineation, description, and conservation in fishes.