Sargassum fusiforme is a macroalga of commercial importance in Eastern Asia, and understanding the reproductive strategy of this macroalga is necessary for conservation and recovery. Here, we used a population genetics approach to identify the reproductive strategy of S. fusiforme. To do this, we performed two sampling procedures: random sampling and quadrat sampling. For random sampling, we collected 80 samples at > 1 m intervals in Site A, B, C and D apart 700 m from each other. For quadrat sampling, we collected 207 samples using 50 cm × 50 cm quadrats comprising 10 cm grid, in two sites Site B and D. Clonemates within these samples were identified by genotyping using 14 (random sampling) or 13 microsatellites (quadrat sampling). For samples obtained by random sampling, only three clonal pairs were detected. For samples obtained by quadrat sampling, each quadrat contained 4–7 genets, and the size was 23.2 ± 14.3 cm (standard deviation) on average and 70.7 cm at maximum. Levels of asexuality was higher in Site B than in Site D, perhaps due to longer exposure time. Site B located rear edge of the intertidal zonation of this species. Over 65% of gene flow via sexual reproduction was limited to within the quadrats, whereas at least 10% extended for meters to kilometers. Taken together, these results suggest that S. fusiforme disperses its offspring sexually and asexually on a small scale, and sexually on a larger scale, with levels of asexuality varying depending on the stress originate from exposure.