Four-season surveys of macroalgal assemblage structure on a coral reef in southern Taiwan were performed by transect investigation from October 1999 through August 2000. Species richness increased over time, and percentage cover and biomass peaked in April. Non-metric multidimensional scaling ordination analysis of species similarities between stations showed three distinct clusters corresponding to the upper reef flat, the lower reef flat and the reef slope. The macroalgal assemblage on the lower reef flat was further grouped into two clusters corresponding to the warmer months (October 1999 and August 2000) and the cooler months (January and April 2000), suggesting the macroalgal assemblage is structured primarily by zone and secondarily by season. Species richness, percentage cover, biomass, species diversity (H') and evenness (J') were highest on the lower reef flat, reflecting greater complexity in the macroalgal assemblage in this zone. However, species diversity and evenness on the lower reef flat and the reef slope did not show seasonal variations. Species diversity in the upper reef flat decreased in the warmer months due to the dominance of an unknown red alga in October 1999 and Enteromorpha linza in August 2000. The results of ANOSIM tests showed that species structure was different not only between zones but also between seasons, and the SIMPER analyses showed that, in the warmer months, Gracilaria coronopifolia , Enteromorpha linza , Laurencia spp. and Hypnea charoides were the species that separated the lower reef flat assemblage from other assemblages. In the same way, the unknown red alga (for October 1999), Enteromorpha linza (for August 2000), Halimeda spp., Mastrophora rosea and Portieria hornemannii were the species responsible for differences in structure between the upper reef flat and the reef slope. In the cooler months, the species responsible for differences in structures between the upper reef flat and the other two zones were Sargassum spp., Gracilaria coronopifolia , Enteromorpha linza and Padina australis , and those responsible for differences between the upper reef flat and the reef slope were Hypnea charoides , Halimeda spp., Mastophora rosea , Enteromorpha linza and Portieria hornemannii . The present investigation suggests that macroalgal abundance and structure on a coral reef in Nanwan Bay in southern Taiwan have marked spatial zonation and seasonal variations, and Sargassum on the lower reef flat has become the most abundant alga, as compared to 12 years ago.