Island endemic species have a much higher risk of extinction than those of mainland. The phoenix damselfly (Pseudolestes mirabilis Kirby, 1900), the single representative of the family Pseudolestidae (Insecta: Odonata) which is endemic to Hainan Island, is facing a danger of extinction along with the acceleration of urbanization. To investigate population genetics and further evaluate the conservational importance, the mitochondrial gene COI of 126 individuals from 11 populations of the phoenix damselfly were sequenced and analyzed. This is the first comprehensive population ecological study for this species. The results recovered low genetic diversity and weak phylogeographic structure. Multiple lines of evidence including neutrality test, mismatch distribution analysis, phylogenetic topologies, and Bayesian skyline plot supported a population expansion just after the Last Glacial Maximum. Statistics of genetic diversity, gene flow, and potential habitats reconstruction suggested that the refugia constricted to the south central areas of the island. Meanwhile, the small population size and low genetic variation in some peripheral populations also implied a niche reduction. Increasing human activity and severe environment destruction may be the main reasons causing a recent decline of the population and increasing the risk of extinction. Therefore, urgent conservational efforts must be implemented to ensure the long-term survival of P. mirabilis. The present research has provided a way to prioritize and assess management strategies of this charismatic species.