Fungal communities inhabiting live, senescent, and decaying leaf sheaths, stems, and leaf blades of standing plants of Spartina maritima in two Portuguese salt marshes were assessed by morphological identification of fruiting structures and sequence-based identification based on polymerase chain reaction (PCR)-cloning analysis of the internal transcribed spacer (ITS) rDNA. The molecular method enabled identification of infrequent ascomycetes and basidiomycetes (filamentous and yeasts) and the asexual morph of Byssothecium obiones and Phaeosphaeria halima. The occurrence and ecological role of the most frequent fungi on different S. maritima substrates seem to depend on the phase of plant life cycle, and specifically on the availability and microenvironmental conditions of each plant substrate. Specifically, By. obiones, Natantispora retorquens, and Lulworthia sp. 1 were involved in the decay of lower-middle culms, Buergenerula spartinae of middle culms and leaves, P. halima, Phaeosphaeria spartinicola, and Stagonospora sp. 1 of middle-upper leaves, and Mycosphaerella sp. I of upper leaves of early-decaying S. maritima plants. The presence of these fungi on live vegetative structures suggests that they might begin the colonization process as endophytes, gaining a competitive advantage over the other saprobic fungi on the plants.