Abstract:In the winter of 2007–2008, a large number of fish were killed by chilling damage that occurred in the Pescadores (Penghu Archipelago). Such extreme weather events can cause rapid population changes, which provide an opportunity to understand the possible restoration mechanism of coral reef fishes in the Pescadores. The fine-scale genetic structure of the rabbitfish, Siganus fuscescens (Siganidae), was assessed using amplified fragment length polymorphism analysis. Significant genetic differences (lower gene flow) were observed between rabbitfish from the northern and southern parts of the Pescadores (Chenkong-Soukang, ΦST 0.075, P < 0.001) but not between those from the northern Pescadores and northeastern Taiwan (Chenkong-Keelung, ΦST 0.03, P > 0.02). The northern Pescadores and northeastern Taiwan have been shown to be relatively connected. The population structure of rabbitfish has complemented and helped support fish population recovery after several chilling events in the Pescadores.