Abstract: This study investigated the genetic structure, genetic diversity and gene flow of the Acanthaster solaris in Xisha Islands and Luhuitou, Hainan Island, using two mitochondrial molecular markers (COⅠ gene sequence and CR sequence in control area). Results showed that CR sequence polymorphism was much higher than COⅠ gene sequence polymorphism, and both markers indicated the highest genetic diversity in Dongdao Island and the lowest in Luhuitou, demonstrating a gradual decline in diversity from the southeast to the northwest. Haplotype analysis indicates that all A. solaris populations in both Xisha and Luhuitou may have originated from a single ancestral haplotype. Compared to COⅠ haplotypes, CR haplotypes were more evenly distributed across populations. There was at least one gene flow direction from south to north, as well as outward migration and diffusion from the central Xisha Islands, but the gene flow in the reverse-direction was minimal. These findings provide theoretical foundation for predicting and managing future outbreaks of A. solaris in Xisha Islands and Luhuitou region.