The study of spatial patterns is important in understanding the causes of the distribution and abundance of organisms, and it also provides a valuable basis for management and conservation. Amphipod crustaceans are key organisms in seagrass ecosystems. However, little attention has been paid to the spatial scales at which amphipod assemblages may vary. We examined variability patterns of amphipod populations inhabiting Posidonia oceanica meadows, over spatial scales spanning four orders of magnitude (1 to 1000 meters) and for two consecutive years. This study reports the scales that contributed most to spatial variation of amphipod assemblages and explores the potential processes driving the observed patterns, with particular emphasis on habitat features. The number of species, the diversity, and the density of some species varied substantially across years. For most species the highest spatial variation in density and biomass occurred at small scales (1 and 10 meters). Based on density data, the structure of amphipod assemblages did not differ at any scales investigated. The patchiness that occurred at small scales may have been related to habitat features, but only weakly. Instead, we postulate that amphipod behavioral processes likely represent good explanatory factors. Although, small-scale spatial variability can be an important feature of amphipod assemblages in P. oceanica meadows, some patterns may have gone undetected because they occur at scales smaller than those investigated.