Fine shale particles and retorted shale are waste products generated during the oil shale retorting process. These by-products are small fragments of mined shale rock, are high in silicon and also contain organic matter, micronutrients, hydrocarbons and other elements. The aims of this study were to isolate and to evaluate fungal diversity present in fine shale particles and retorted shale samples collected at the Schist Industrialization Business Unit (Six)-Petrobras in São Mateus do Sul, State of Paraná, Brazil. Combining morphology and internal transcribed spacer (ITS) sequence, a total of seven fungal genera were identified, including Acidiella, Aspergillus, Cladosporium, Ochroconis, Penicillium, Talaromyces and Trichoderma. Acidiella was the most predominant genus found in the samples of fine shale particles, which are a highly acidic substrate (pH 2.4-3.6), while Talaromyces was the main genus in retorted shale (pH 5.20-6.20). Talaromyces sayulitensis was the species most frequently found in retorted shale, and Acidiella bohemica in fine shale particles. The presence of T. sayulitensis, T. diversus and T. stolli in oil shale is described herein for the first time. In conclusion, we have described for the first time a snapshot of the diversity of filamentous fungi colonizing solid oil shale by-products from the Irati Formation in Brazil.