In recent years, drifting and inundating brown seaweed (Sargassum horneri) biomass, called 'golden tides', has frequently drifted and accumulated along the southern coastlines of Korea, causing devastating impacts on the local economy and coastal ecosystems. In this study, based on combined analyses of mitochondrial DNA cox3 gene and seven microsatellites, we investigated the genetic makeup of the floating S. horneri populations (N = 14) in comparison to Korean benthic populations (N = 5), and tracked their genetic sources. Given a shared mtDNA haplotype and oceanic circulation systems, the floating populations may have been originated from the southeastern coast of China (e.g. Zhoushan, Zhejiang province). Population structure analyses with microsatellites revealed two distinct genetic clusters, each comprising floating and benthic populations. High levels of inter-population differentiation were detected within Korean benthic samples. The floating populations from the same periods during a 2015-2018 year were genetically more different from one another than those from different periods. These results suggest that the floating populations might be of multiple genetic sources within geographic origin(s). This study will inform management efforts including the development of "S. horneri blooming forecasting system", which will assist in mitigating ecological and economic damages on the Korean coastal ecosystems in the future.