Ascomycetous fungi play an important role in the early stages of decomposition of Spartina alterniflora, but their role in the decomposition of other Spartina species has not been investigated. Here we use fingerprint (terminal restriction fragment length polymorphism) and phylogenetic analyses of the 18S to 28S internal transcribed spacer region to compare the composition of the ascomycete fungal communities on early decay blades of Spartina species (Spartina alterniflora, Spartina densiflora, Spartina foliosa, and a hybrid (S. alterniflora x S. foliosa)) collected from three salt marshes in San Francisco Bay and one in Tomales Bay, California, USA. Phaeosphaeria spartinicola was found on all samples collected and was often dominant. Two other ascomycetes, Phaeosphaeria halima and Mycosphaerella sp. strain 2, were also common. These three species are the same ascomycetes previously identified as the dominant fungal decomposers on S. alterniflora on the east coast. Ascomycetes appeared to exhibit varying degrees of host specificity, demonstrated by grouping patterns on phylogenetic trees. Neither the exotic S. alterniflora nor the hybrid supported fungal flora different from that of the native S. foliosa. However, S. densiflora had a significantly different fungal community than the other species, and hosted at least two unique ascomycetes. Significant differences in the fungal decomposer communities were also detected within species (two clones of S. foliosa), but these were minor and may be due to morphological differences among the plants.