As a highly resistant polymer family, polyurethanes ( PU) are responsible for increasing environmental issues. Then, PU biodegradation is a challenging way to develop sustainable waste management processes based on biological recycling. Since the metabolic diversity of fungi is a major asset for polymer degradation, nearly thirty strains were isolated from sampling on six different PU wastes‐containing environments. A screening of the fungi on four thermoplastic PU ( TPU) with different macromolecular architectures led to the selection of three strains able to use two polyester PU as sole carbon source: Alternaria sp., Penicillium section Lanata‐Divaricata and Aspergillus section flavi. Weight loss, FT‐ IR, Scanning Electron Microscopy and Size Exclusion Chromatography analyses revealed that these three fungi degrade slightly and similarly a fatty acid dimer‐based TPU while variability of degradation was noticed on a polycaprolactone‐based TPU. On this last TPU, robust analysis of the degraded polymers showed that the Penicillium strain was the best degrading microorganism. Membrane enzymes seemed to be involved in this degradation. It is the first time that a strain of Penicillium of the section Lanata‐Divaricata displaying PU biodegradation ability is isolated. These newly discovered fungi are promising for the development of polyester PU waste management process.