Fungal decomposers are important contributors to the detritus-based food webs of salt marsh ecosystems. Knowing the composition of salt marsh fungal communities is essential in understanding how detritus processing is affected by changes in community dynamics. Automated ribosomal intergenic spacer analysis (ARISA) was used to examine the composition of fungal communities associated with four temperate salt marsh plants, Spartina alterniflora (short and tall forms), Juncus roemerianus, Distichlis spicata and Sarcocornia perennis. Plant tissues were homogenized and subjected to a particle-filtration protocol that yielded 106 microm particulate fractions, which were used as a source of fungal isolates and fungal DNA. Genera identified from sporulating cultures demonstrated that the 106 microm particles from each host plant were reliable sources of fungal DNA for ARISA. Analysis of ARISA data by principal component analysis (PCA), principal coordinate analysis (PCO) and species diversity comparisons indicated that the fungal communities from the two grasses, S. alterniflora and D. spicata were more similar to each other than they were to the distinct communities associated with J. roemerianus and S. perennis. Principal component analysis also showed no consistent, seasonal pattern in the composition of these fungal communities. Comparisons of ARISA fingerprints from the different fungal communities and those from pure cultures of selected Spartina ascomycetes supported the host/substrate specificity observed for the fungal communities.