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Field and laboratory studies were used to elucidate the factors affecting temporal and spatial variations of species abundance and structure of macroalgal assemblage and environmental variables between fish farming (FFA) and non-fish farming (NFFA) areas in Hsiao-Lu-Chiao island, a coral island in southwestern Taiwan. Four experiments have been approached: 1. field surveys of macroalgal assemblage structure on 5-m and 10-m depth at 3 sampling sites at FFA (FFA1, FFA2 and FFA3) and 1 sampling site at NFFA from September 2004, January 2005 and April 2005; 2.the relationship between abiotic (monthly maximum air temperature, monthly minimum air temperature, monthly mean air temperature, monthly cumulative precipitation, monthly cumulative irradiance, seawater temperature, light extinction coefficient, water motion, and nutrient (NO3-, NO2-, NH4+, SRP, DON, and DOP) and biotic (seaurchin density) factors and spatio-temporal variations in macroalgal structures analyzed by non-parametric multivariate model; 3. Factors affecting macroalgal abundance and structure: (1). Comparison of growth temperature ranges in different species to field temperature fluctuation; (2).Comparison of growth irradiance ranges in different species to field irradiance fluctuation; 4.Herbivore pressure: (1). Spatio-temporal variations of sea urchin abundance and structure of assemblage; (2). Gut contents and food preference of sea urchin experiment; (3). Herbivore exclusion experiment. Macroalgal %cover, biomass, species richness, diversity (H¡¦) and evenness (J¡¦) showed temporal and spatial variations, low values in January 2005 and also low values in the 5 m- and 10 m-depth areas of FFA1 and the 10 m-depth areas of FFA2. The data of k-dominance curve, hierarchical cluster and ANOSIM tests indicate that macroalgal assemblage is different between 4 sampling sites, between 2 depths and between 3 seasons. Ceratodictyon spongiosum is the most important species that separates September and January assemblages from April assemblage and separates the FFA1 and FFA2 assemblages from the FFA3 and NFFA assemblages. BVSTEP analysis shows that nutrients (NO3-, DON, DOP), temperature, monthly cumulative precipitation, and sea urchin density are the factors corresponding to variations of macroalgal assemblages, this correlation is more significant for 5 m-depth assemblage. Fish farming area FFA1and FFA2 assemblage are affect by sea urchin density, temperature and DON. Sea urchin influnces macroalgal abundance and assemblage structure in FFA1 and FFA2. Macroalgal %cover in 5 m-depth area shows a reversal relationship with sea urchin density; however, this relationship is not observed for 10 m-depth area. FFA1 and FFA2 are belong to high grazing pressure sites as indicated by high sea urchin density and exclusion experiment. Sea urchin gut contents and feeding preference test show that sea urchin has strong food selectivity with Hypnea charoides and Gracilaria coronopifolia as the most preferred species. Herbivore exclusion experiment shows that Hypnea charoides and Gracilaria coronopifolia are the species recruited in the cages. Ceratodictyon spongiosum had high biomass in FFA1 and FFA2 in January, which was ¡¥low DOP/high DON¡¦. The coindicence of temporal variations in FFA3 assemblage structure with a change from ¡¦Halimeda opuntia and Boodlea compostia¡¦ ¡÷ ¡¦Amphiroa fragilissima, Corallina phhulifera and Galaxaura oblongata¡¦ ¡÷¡¦Halimeda opuntia and Boodlea compostia¡¦ with low nitrogen/ high phosphorous¡¦ ¡÷¡¦ high nitrogen/ low phosphorous¡¦ ¡÷ ¡¦low nitrogen/ high phosphorous¡¦ suggest a role of ¡¦low nitrogen (NO3-)/high phosphorous (DOP)¡¦ for FFA3 structure modification. NFFA assemblage is controlled by temperature and monthly cumulative precipitation. Monthly cumulative precipitation in September was higher than January and April, in which Boodlea compostia and Gracilaria coronopifolia were dominant algae in September. The temperature growth responses of algae using the continuous-flow outdoor laboratory tank culture system fit their seasonal growth, reflecting the temperature-dependent manner of seasonal variations in abundance. It could be concluded from the present investigation that the structure of benthic macroalgal assemblage in Hsiao-Lu-Chiao island in southwestern Taiwan is affected by predicted natural and pulse disturbances. Temperature fluctuations involve in overall temporal variations in structure. Sea urchin herbivory and nutrient as pulse nutrient modulate the structure in fish farming area while monthly cumulative precipitation is associated with algal structure in non-fish farming area.