Filamentous fungi were isolated from estuarine sediments collected from two contaminated sites. One site was contaminated mainly by polycyclic aromatic hydrocarbon (PAH) with a concentration around 407 mug g(-1) of different PAHs, and the other by different sources of industrial pollutants; both were compared to a pristine site. All three sites were located in the Baixada Santista, Sao Paulo State, Brazil. The aim of the present investigation was the isolation of filamentous fungi from pristine and industrially polluted sediments in order to assess the mycobiota present in those sites and to evaluate their tolerance to phenanthrene and pyrene. Most of the isolated fungi were mitosporic ascomycetes, including Aspergillus sp., Chrysosporium sp., Cyclothyrium spp., Gliocladium sp., Penicillium spp., Phoma spp., and Trichoderma spp. There were also representatives of sexual Ascomycetes, Basidiomycetes, and Zygomycetes. The results showed that 59% of the evaluated fungi were tolerant to pyrene and 30% to phenanthrene. Representatives of Trichoderma were the most tolerant among the filamentous fungi investigated. A representative of Penicillium simplicissimum was the only isolate tested that had a better growth in the presence of pyrene than in its absence.123345356