Thermophilic fungi constitute an ecologically well-defined group, commonly found in environments wherever decomposition of organic matter takes place, making them self-heating. The importance of thermophilic fungus in ecosystems contrasts with the incompleteness of our understanding of the group's biogeography patterns, phylogenies and coevolution relationships. Actually, the lack of data about thermophilic fungi from the Brazil is a limiting factor that also contributes for this scenario. In order to reduce this gap of knowledge, we aimed to characterize thermophilic filamentous fungi in Araucaria Forest, Atlantic Forest biome. Species identification was achieved by using internal transcribed spacers (ITS) as molecular ribosomal markers. In total, 240 heat-tolerant fungal strains were isolated and identified as Thermothielavioides terrestris, Thielavia sp., Thermoascus crustaceus, Aspergillus fumigatus, Rhizomucor miehei, Rhizomucor pusillus, and Rhizopus microsporus. All thermophilic strains exhibited optimal growth at 45 °C. T. crustaceus, T. miehei e R. pusillus were the dominant species, with the frequencies of occurrence of 35.00%, 28.33% and 23.33%, respectively. Our data reveals the apparent diversity of the Neotropical realm and may serve as reference to future studies that will try to elucidate important aspects of group.