Many deep-sea scientific discoveries have been driven by sampling from mooring systems. We observed biofouling assemblages on five mooring systems in the Talaud Sea and the Halmahera Sea. Biofoulings on all the mooring components extending from the sea surface to the depth of 1800–2000 m were documented. We found mollusks, barnacles, annelids, algae, and sponges assemblages on buoys, instruments, and cables of the mooring systems. Barnacle Heteralepas sp. was the most dominant biofouling attached to the float instruments of all mooring systems. At a depth of 200 m, we found mollusks, barnacles, and sponges; while algae were founded at a depth of 750 m, 1000 m, 1200 m, and 1800 m. In comparison, sponges were detected at a depth of 200 m, 250 m, 500 m, 750 m, 1000 m, 1200 m, and 1800 m. Nevertheless, at a depth of 2000 m, we did not find any biofouling attached to the mooring systems.