Polychaetes constitute most of the benthic macroinvertebrates in estuarine and coastal environments. We investigated the utilization of organic matter in two polychaete species, Capitella sp. I and Perinereis nuntia brevicirris, living in different coastal habitats. The protease activity of Capitella sp. I (89.7 μg mg−1) was about 10 times that of P. nuntia brevicirris (8.0 μg mg−1). High cellulase (endo-β-1,4-glucanase) activity was detected in P. nuntia brevicirris (3.2 μg mg−1), whereas scarcely any was detected in Capitella sp. I. We isolated cDNA clones of protease mRNA from Capitella sp. I and of cellulase mRNA from P. nuntia brevicirris. The high protease activity of Capitella sp. I enabled it to survive in the sediment under a fish farm, where it degrades organic matter. In contrast, the high cellulase activity of the estuary-dwelling P. nuntia brevicirris allowed it to degrade organic matter originating from terrestrial areas.