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This study investigated the genetic population structure of the regionally endemic rainforest fish Cairnsichthys rhombosomoides by analysing sequence variation in the mitochondrial control region. The results indicated that individual populations, even those located in close proximity (5 km), were highly distinct. The pattern of genetic structure cannot be explained by physical barriers to gene flow and was not consistent with models based on separation of populations by distance or any hierarchical structuring within the riverine network. The management implications of the observed genetic structure are discussed.