Invasive species are receiving increased attention both for their direct effects, including competitive displacement and predator-prey interactions, and indirect effects involving ecosystem and habitat alterations. The common reed Phragmites australis is spreading along much of the Atlantic and Gulf coasts of the USA. Its spread is particularly apparent in disturbed oligohaline to mesohaline areas, where it may displace the marsh cordgrass Spartina alterniflora. Because of the different morphologies of these plants, associated sediment effects, and differences in biogeochemical cycling, there is the potential for significant faunal community changes where macrophyte species replacement occurs. We conducted a study in the mesohaline region of Chesapeake Bay to examine differences between benthic communities associated with S. alterniflora and P. australis marshes. Paired P. australis and S. alterniflora marshes were sampled at 4 sites in summer and 2 sites in fall, blocking for tidal height (high marsh versus low marsh) and small-scale topographic features (rivulet and hummock areas in each marsh type). Sediment grain size did not differ between marsh types, and percent organics differed only for P. australis hummock sites compared to other habitat types. Benthic microalgal biomass also did not differ among marsh types. There was only a small effect on faunal abundance patterns, with most species exhibiting slightly higher mean density in Spartina compared to adjacent Phragmites marshes. Much stronger differences in faunal density were observed between hummocks and adjacent rivulets within each marsh type. While macrophyte type had a detectable effect, local microhabitat characteristics had a stronger relation to local faunal abundance patterns. Since such microhabitat characteristics may covary with macrophyte type (although they did not do so in this study), care must be taken in the design and interpretation of comparative marsh studies and more emphasis should be given to including relations of small-scale topographic features with faunal characteristics. In this system and on the scale studied here, macrophyte replacement did not strongly affect the benthic infaunal community.