The purpose of this study was to examine the usefulness of electron paramagnetic resonance spectroscopy (EPR) to estimate zinc and copper ions biosorption from the environment by pigmented soil fungi Cladosporium cladosporioides. The existence of a low amount of pheomelanin, besides eumelanin, in C. cladosporioides samples was proved by the analysis of shape of their EPR spectra. Concentration of o-semiquinone free radicals in crude mycelium was 2.4×10¹⁷ spin/g. Changes in free radicals system of C. cladosporioides cultured in the presence of Zn²⁺ and Cu²⁺ were analysed. Both magnetic and chemical interactions of zinc and copper ions with free radicals in C. cladosporioides melanin were found. Magnetically interacting diamagnetic Zn²⁺ ions increased the concentration of o-semiquinone free radicals in melanin existing in C. cladosporioides mycelium, whereas paramagnetic Cu²⁺ ions decreased this concentration. Chemical interactions of Zn²⁺ and Cu²⁺ ions decreased the free radical concentrations in C. cladosporioides melanin. Homogeneously distributed free radicals in C. cladosporioides melanin rise its activity in biosorption processes.