Epifaunal invertebrates are sensitive to changes in the identity of the dominant host plant, so assessing differences in the structure of epifaunal assemblages is particularly pertinent in areas where seagrasses have been replaced by alternative vegetation (e.g. green seaweeds). In this study, we aimed to compare the diversity, abundance and structure of epifaunal assemblages, particularly amphipods, between meadows dominated by the seagrass Cymodocea nodosa and the green rhizophytic algae Caulerpa prolifera on shallow soft bottoms of Gran Canaria Island, determining whether patterns were temporally consistent between two times. The epifaunal assemblage structure (abundance and composition) consistently differed between both plants, those assemblages associated with C. prolifera-dominated beds being more diverse and abundant relative to C. nodosa meadows. Amphipods constituted ~70% of total crustaceans for the overall study, including 37 species belonging to 16 families. The amphipod abundance was ~3 times larger in C. prolifera-dominated beds than in C. nodosa meadows. We detected species-specific affinities; for example, Microdeutopus stationis, Dexamine spinosa, Aora spinicornis, Ischyrocerus inexpectatus and Apherusa bispinosa were more abundant in C. prolifera-dominated beds; while the caprellid Mantacaprella macaronensis dominated in C. nodosa meadows. However, some species, such as Pseudoprotella phasma and Ampithoe ramondi, were found in both habitats with varying abundances between times.