β Diversity is an ecological concept used to describe the turnover of species across a wide range of spatial and temporal scales, but such knowledge is lacking for macroalgal assemblages of the Red Sea. β Diversity patterns for Red Sea macroalgae were evaluated from different sites (Hurghada, Safaga, and Al-Quseir) and seasons across different environmental disturbances. β Diversity was studied by partitioning the total number of species (γ diversity) into additive components. Geographical heterogeneity was more important than seasonal heterogeneity in structuring macroalgae both at species and functional group levels. Species replacement as a component of β diversity produced dissimilarity in species composition and taxonomic structure. Replacement of species between sites was responsible for the presence of new functional groups of macroalgae. High β diversity and taxonomic similarity values were characteristic of the macroalgae of the Red Sea. The occurrence of small macroalgal thalli that have short life cycles induced high species replacement and subsequently high β diversity, with spatial heterogeneity and environmental gradient as drivers of β diversity. Anthropogenic disturbance at the Safaga site was suggested to induce variation of macroalgal assemblages and functional groups. Excluding rare species from the data set did not change the high values of b diversity.