Aim: Hainan Island, southern China, is characterized by rich diversity and endemism of marine organisms, yet the underpinning mechanisms and processes contributing to speciation and diversification are poorly understood. Here, the brown alga Sargassum polycystum is used as a model to identify putative marine glacial refugia and explore biogeographical patterns driven by climate change in the late Pleistocene ice ages. Location: South-East Asia. Methods: Mitochondrial cox1 and cox3 and nuclear internal transcribed spacer-2 (ITS2) were obtained from 310, 325 and 313 individuals of S. polycystum (23 localities), respectively. Phylogenetic trees (maximum likelihood and Bayesian inference) and haplotype/ribotype networks were constructed to elucidate phylogeographical patterns. Analysis of molecular variance (AMOVA), neutrality tests (Tajima's D and Fu & Li's D*), current (θπ) and historical (θw) genetic diversities and extended Bayesian skyline plots (EBSP) were used to estimate historical demography. Results: The populations from the south-west of Hainan Island harboured much higher genetic diversity and unique endemism in comparison with other populations in the distribution range. Sargassum polycystum experienced relatively long-term stable population size followed by a continued period of demographic expansion in the late Pleistocene. Main conclusions: Our phylogeographical evidence revealed the existence of a previously unidentified marine refugium specific to S. polycystum in the south-west of Hainan Island, China (the Central Depression of the Yinggehai Basin), along with a possible secondary refugium around the Bali Island, Indonesia. These biogeographical findings provide important insights regarding speciation, adaptation and evolution of marine organisms in South-East Asia and the conservation of unique biodiversity under climate change.