Low-elevation islands face threats from sea level rise (SLR) and increased storm intensity. Evidence of endangered species’ population declines and shifts in vegetation communities are already underway in the Florida Keys. SLR predictions indicate large areas of these habitats may be eliminated in the next century. Using the Florida Keys as a model system, we present a process for evaluating conservation options for rare and endemic taxa. Considering species characteristics and habitat, we assess central issues that influence conservation options. We contrast traditional and controversial options for two animal and two plant species giving special emphasis to perceptions of ecological risk and safety from SLR and suggest courses of action. Multiple strategies will be required to spread extinction risk and will be effective for different time periods. Global climate change presents an uncertain, perhaps no-analog future that will challenge land managers and practitioners to re-evaluate equilibrium-state-conceived laws and policies not only for these taxa, but for many facing similar threats. To embrace conservation in a changing world will require a new dialogue that includes controversial ideas, a review of existing laws and policies, and preparation for the oncoming change.