The endangered soft coral Dendronephthya australis faces substantial population decreases in central eastern Australian waters. Despite uncertainty about the cause of these declines, the population genetics of the species has not been investigated. Genetic analysis suggests that D. australis is a single species within the family Nephtheidae, confirming identifications based on morphological characteristics only. Soft coral colonies were distributed from Seahorse Gardens in Port Stephens to Jervis Bay in temperate Australian waters, a distance of some 400 km. Genetic differentiation was observed along this distribution using SNP genotyping. Relatively high levels of genetic differentiation were observed between Jervis Bay and the other sites, indicating limited gene flow between this location and others. Moreover, the genetic distinctiveness, low diversity and heterozygote excess at this southern location suggested that it was subjected to a recent population decline and genetic bottleneck. Colonies at Seahorse Gardens and Ettalong, approximately 150 km south of Seahorse Gardens, displayed greater genetic diversity, making these sites more likely to host ancestral populations and to have acted as refugia. Recent substantial decreases in population sizes at these locations are particularly concerning, and these locations require immediate conservation attention
