Thermokarst activity at permafrost sites releases considerable amounts of ancient carbon to the atmosphere. A large part of this carbon is released via thermokarst ponds, and fungi could be an important organismal group enabling its recycling. However, our knowledge about aquatic fungi in thermokarstic systems is extremely limited. In this study, we collected samples from five permafrost sites distributed across circumpolar Arctic and representing different stages of permafrost integrity. Surface water samples were taken from the ponds and, additionally, for most of the ponds also the detritus and sediment samples were taken. All the samples were extracted for total DNA, which was then amplified for the fungal ITS2 region of the ribosomal genes. These amplicons were sequenced using PacBio technology. Water samples were also collected to analyze the chemical conditions in the ponds, including nutrient status and the quality and quantity of dissolved organic carbon. This dataset gives a unique overview of the impact of the thawing permafrost on fungal communities and their potential role on carbon recycling.