The responses of tidal marsh macroinvertebrate assemblages to the conversion of Spartina alterniflora marshes to marshes dominated by the invasive reed, Phragmites australis, are poorly understood. Changes in edaphic, vegetative, hydrologic, and detrital conditions that attend conversion to Phragmites should produce changes in the intertidal fauna. We used core sampling (7.8-cm diameter, 4-cm deep) and litter packs to compare the intertidal macroinvertebrate fauna of Phragmites marshes and adjacent remnant Spartina marshes in a brackish reach of the Mullica River (0–17 ppt salinity during the study) in southern New Jersey, USA. Detrital and above-ground vegetative biomass and water velocity were greater in Phragmites marsh; stem density, microtopographic relief, and the density of standing-water microhabitats were greater in Spartina marsh. The intertidal assemblages varied between marsh types. Total macroinvertebrate density was greater in Spartina marsh (97,000 m⁻²) than in Phragmites marsh (82,000 m⁻²). Mean taxa richness (number of taxa per core sample) was greater in Spartina marsh (12.4 taxa sample⁻¹) than in Phragmites marsh (9.4 taxa sample⁻¹) and dominance (relative abundance of the three most abundant taxa) was lower. Oligochaeta, Nematoda, and the polychaete, Manayunkia aestuarina, dominated the fauna (>75% of the total abundance) in both marsh types. Of these, oligochaetes were more abundant in Spartina marsh, and nematodes and polychaetes were slightly more abundant in Phragmites marsh. Most common subdominant taxa (100–4,000 m⁻²), including ceratopogonids, chironomids, mites, ostracods, isopods, and gastropods were more abundant in Spartina marsh. Collembolans were more abundant in Phragmites marsh; amphipods were about equally abundant in both marsh types. Invertebrate abundance and assemblage composition varied with distance from the edge of the marsh in both marsh types; overlap in assemblage composition between marsh types was greatest at the edge of the marsh, where more frequent inundation may have moderated the influence of vegetation type on the marsh fauna. For mean taxa richness and for the density of most taxa, the effect of marsh type on density exceeded the effect of season, marsh position, or a local salinity gradient. We consider the greater density of intertidal standing-water microhabitats and probably of microalgal production as important sources of faunal variation between marsh types. Fewer refugia from predators during high tide in Phragmites marsh may also contribute to variation in faunal abundance and community structure between marsh types. Detritus biomass was probably a more important source of spatial variation in the fauna of the Phragmites marsh than in Spartina marsh.