Legislative and regulatory frameworks for conserving biodiversity often focus on the species as a fundamental unit for protection. In cases where the taxonomic or conservation status of a species is uncertain, the precautionary principle may be invoked in listing suspected but as yet undescribed taxa as vulnerable or endangered. In this paper, we present an evaluation of the taxonomic status of what has been regarded as a distinctive but as yet undescribed species of freshwater turtle, declared endangered in the Action Plan for Australian Reptiles and vulnerable in the schedules of state and federal conservation acts. Using mitochondrial sequence variation, we show that the Bellinger River turtle is an unremarkable population of a common and widespread species, Emydura macquarii. In addition, we present evidence suggesting that it may have been recently introduced to, or may be a recent invader of, the Bellinger River (New South Wales, Australia) where it may come to compete with Myuchelys georgesi, an endemic found only in the Bellinger River. Our study illustrates the need to couple fundamental research with on-ground action early in an adaptive management context, particularly where taxonomic status of the target species is uncertain. Short-term cost savings of failing to do so may come to be greatly exceeded by longer-term opportunity loss where conservation dollars are limited.