Context Despite the key ecological role played by epifaunal communities associated with macroalgae in temperate coastal rocky shores worldwide, biodiversity and ecological patterns of their associated invertebrate communities are still poorly known. Aims The present study aims to compare the amphipod assemblages associated with the dominant canopy-forming macroalgae in shallow subtidal habitats of the Alboran Sea, as well as to explore its biogeographical patterns and the influence of protection measures. Methods Replicate samples of both Ericaria selaginoides (=Cystoseira tamariscifolia) and Halopteris scoparia were collected at two different bioregions within the Alboran Sea and both inside and outside marine protected areas. Key results Amphipoda was the dominant taxon within the mobile epifaunal community, both in terms of number of species (47 different species were recorded) and individuals (>70% of the total abundance). Assemblages associated with E. selaginoides and H. scoparia differed and showed a marked response to the Mediterranean–Atlantic gradient in this region; species related to warmer waters become increasingly dominant towards the east. However, there were no significant differences in amphipod assemblage composition, abundance or species richness between protected and non-protected areas. Conclusions Obtained results highlighted the relevance of these native macroalgae as habitat for epifauna, as well as the influence of macroalgal identity and regional biogeographical patterns on amphipod distribution. Implications This study provides valuable baseline information to monitor human-induced changes such as coastal pollution, invasive species, and climate change. It also draws attention about the uncertain response of epifaunal communities to management strategies (such as marine protected areas) and ecological processes (e.g. increasing predation pressure).