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The present study was aimed at characterising species diversity of fungi inhabiting petroleum-contaminated soils of oil fields in a southern region of Iran. Two different techniques were used for fungal isolation including enrichment on atmospheres of phenolic hydrocarbons and crude oil as substrate. Phylogenetic analysis of the internal transcribed spacer of ribosomal DNA was used for taxonomic identification with additional information from the β-tubulin gene for selected taxa. Overall, 183 strains from 14 genera and five orders were obtained: Pleosporales (Alternaria, Curvularia, Stemphylium, Ulocladium), Chaetothyriales (Exophiala), Eurotiales (Aspergillus), Hypocreales (Acremonium, Emericellopsis, Sarocladium, Stachybotrys, Fusarium, Trichoderma, Beauveria), and Capnodiales (Cladosporium). The most frequently isolated strains belonged to the genera Alternaria, Exophiala and Aspergillus. The crude oil substrate was the most successful isolation method, and among the four hydrocarbon enrichments, toluene substrate yielded the highest number of strains. Enrichment on xylene and benzene also yielded herpotrichiellaceous and other filamentous fungi.