The invasion of Phragmites australis (common reed) into Spartina alterniflora (cordgrass) salt marshes along the northeastern coast of the United States has recently been of concern. Numerous studies have evaluated the effects of P. australis on marsh nekton and infauna, but its effects on the distribution of stem-dwelling epifaunal communities has not been investigated previously. Standing living and dead plants of both species were collected periodically during three growing seasons (2000–2002) from brackish and salt marshes in New Jersey and Long Island, and the abundance, composition, and diversity of epifaunal communities associated with the stems of the two plant species were compared. Spartina alterniflora, particularly dead S. alterniflora, supported a higher density of animals than P. australis in 12 of the 19 samplings. When communities on standing live and dead stem were considered separately, higher abundances were found on dead S. alterniflora stems. Nematodes and harpacticoid copepods were the dominant taxa, with mites, annelids, and insects comprising minor components. Taxon-specific abundances tended to be higher on S. alterniflora stems, and community diversity was generally greater on this species as well. Between-site and between-year variation was observed. Relative to data recorded from sub-tropical salt marshes, the epifaunal communities in our samples were less abundant and diverse. Differences in the epiphytic communities associated with the two species, along with differences in stem structure, may explain why S. alterniflora stems support more epifaunal animals than P. australis stems overall.