The structure and diversity of sixteen macroalgal assemblages originating from two coastal locations in the Northern (Kavala gulf) and Central (Maliakos gulf) Aegean in Greece were explored by examining their relative abundance distributions (RADs) and fitting five stochastic niche-based models. A mechanistic interpretation of the underpinning assembly processes was attempted by relating the assumptions of the fitted models with available abiotic data corresponding to each assemblage. The random fraction niche-based model, assuming a random niche apportionment to species, was fitted to the majority of Maliakos assemblages characterized by more evenly distributed and speciose RADs, whereas the random assortment model, assuming no relationship among species abundance and niche size, was fitted to most of the Kavala assemblages characterized by steeper RADs with fewer species. Among the possible underlying mechanisms, wave exposure seems to play a key role in macroalgal assembly processes; however factors such as biogeography and hard substrate availability must be also taken into consideration. Short-term processes as changes in resource availability (nutrients and light), known as drivers of assembly rules in other primary producers (e.g. phytoplankton), do not considerably affect macroalgae in the oligotrophic Eastern Mediterranean, possibly due to their longer life spans.