AxIOM is a sample-based dataset (n = 187 samples) documenting occurrences of amphipod crustaceans associated to Posidonia oceanica seagrass meadows from Mediterranean Islands (Corsica, Sardinia). In total, it contains 10720 records of specimens belonging to 72 species spanning 29 families. Samples were collected over different periods 3 consecutive years, both during the day and during the night. A nested hierarchical sampling design was set up, and multiple sampling methods were combined to ensure a holistic view of the taxocenosis. The dataset package is composed of two data files: one describing sampling events, and the other reporting occurrence data of amphipod crustaceans.