There are high rates of regional and global extinctions among freshwater species and few chances for recovery. We report here on the rediscovery after 30. years of a small fish, the southern-purple spotted gudgeon (Mogurnda adspersa), once widespread in the southern Murray-Darling Basin of south-eastern Australia. The rediscovery was in a region, the Lower Murray, where temperate riverine and wetland habitats are modified by a broad spectrum of changes including intensive flow regulation and diversions. There was some doubt whether the rediscovered population was a true remnant or a recent introduction, particularly as there was a translocated population in a nearby artificial habitat. Fortunately, a non-government organisation acted to rescue into captivity about 50 specimens as the remaining wetland habitat dried completely, soon after rediscovery, as a consequence of a decade-long drought and water diversions. We describe the habitat and ecology of fish in the rediscovery site, and provide genetic data, both nuclear (50 allozyme loci) and mtDNA (1141 base pairs; two genes), to show that they were true remnants of the regional native population. This information allows clear planning for future recovery including reintroductions, and is a case study that provides strategies, and hope, for conservation and management concerning other modified habitats. Specifically, it highlights the need for a rapid response to conserve threatened species, the recognition of remnant natural values in altered environments, and the treatment of new finds as native until there is alternate evidence.