Fungi are important actors in the ecological processes occurring in mangroves and are thought to play a role in organic matter decomposition pathways, despite the fact that a large fraction of the carbon processing in mangroves happens in the anoxic bulk sediment. The fungal diversity in these strata is, however, poorly known. Here, using microscopic observations of calcofluor white stained samples, we detected the presence of fungal hyphae indicating that fungal growth was occurring under these anoxic and sulfidic conditions. To assess the fungal diversity we used 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer land 2 (ITS-1 and ITS-2). We analysed approximately 5 000 reads for each ITS, corresponding to around 115 molecular operational taxonomic units. The taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The most abundant operational taxonomic units were affiliated to: a taxon with affinity to the genus Sistotremastrum (Trechisporales), Dipodascus australiensis (Saccharomycetales), an Alternaria species (Pleosporales) and an unknown Lecanoromycete. This study indicates the presence of rich fungal communities in anoxic mangroves sediments. It also raises the question of the adaptation of these organisms to the environmental conditions and of the roles they play in organic matter decomposition processes. (C) 2011 Elsevier Ltd and The British Mycological Society. All rights reserved.