Sargassum muticum is an invasive brown macroalga that originates from Japan. In the introduced range, thalli can grow in soft substratum habitats attached to embedded rock fragments and shells. Within Strangford Lough, Northern Ireland, S. muticum has rapidly colonised large areas of soft substrata, where dispersal by peripatetic or 'stone-walking' plants is very effective. Sediment cores were collected under and outside canopies of S. muticum in Strangford Lough (S. muticum first recorded there in 1995) and Langstone Harbour, English Channel (S. muticum first found there in 1974) to investigate modification of the infaunal assemblages. At both study sites, community analyses highlighted significant differences between the assemblages under the canopies and those in adjacent unvegetated areas. In Strangford Lough, the invertebrate community under the canopy contained a higher abundance of smaller, opportunistic, r-selected species than outside the canopy. By contrast, the communities under and outside the canopy at Langstone Harbour were similar in species composition, diversity and dominance, but overall faunal abundance was greater under the canopy. Sediment characteristics were not affected by S. muticum canopies, but the infaunal changes may be related to environmental modification; shading, flow suppression and temperature stratification were also investigated. The differences between these 2 sites indicate that localised conditions and/or the duration of colonisation of S. muticum are important in determining the nature of habitat modification.