Endangered seahorse genomic data recount a past of enforced isolation and guide future conservation efforts.

Amid a global biodiversity crisis hastened by climate change, it is urgent that species' declines are halted. To design the most effective conservation strategies to address these declines, the nature and timing of the most probable genetic or nongenetic factors behind population collapses need to be identified. We used high-density RADseq genetic markers to determine the demographic history and track population-level exposure of the Knysna seahorse (Hippocampus capensis), the first syngnathid listed as endangered by the International Union for Conservation of Nature (IUCN), to historical and current threats. Our results revealed an initial link between sea-level fluctuations and settlement for this estuarine endemic species that occurred on a coastline without obvious alternative habitats that were followed by divergence and progressive isolation of the extant populations. Two of the three extant Knysna seahorse populations, those inhabiting estuaries most affected by floods and natural or human-mediated breaching of the estuary mouths, showed severe and continued contractions in effective population size. We illustrated the potential of genomics for the conservation of the most vulnerable species and their fragile ecosystems and highlighted the urgency and type of measures required to maintain species' persistence and resilience. Our results provide practical insights to help protect this endangered seahorse, namely, the need for proactive management, which is essential for preventing the expected losses of genetic diversity that follow shrinking effective population sizes. Additionally, we showed that hydrological stability and increased substratum availability can foster recoveries without the need for potentially riskier alternatives such as the recently proposed seahorse translocations.