In this study, microorganisms were isolated from Mihaliccik region (Eskisehir, Turkey) lignites with low rank and high ash and sulphur content. A series of heavy liquids (from 1.3 g/ml to 1.9 g/ml) were used to determine the washability characteristics of lignite sample. Washability data indicated that the physical cleaning of the sample would be difficult. Therefore, microbial desulphurization through native microorganism was performed owing to inadequate physical cleaning. After isolation studies, six different bacteria, five different molds and seven different yeasts were obtained. Desulphurization studies showed that the most effective isolate was a fungus and its molecular identification of the 18S rRNA gene showed that this fungus was Alternaria sp. Cf1 isolate with accession number KF564051. After screening of desulphurization studies, optimisation experiments with this fungal isolate were performed with Taguchi's methodology. The parameters such as particle size, pulp density, initial pH, inoculum amount, incubation time were investigated during optimisation studies and optimum values were found as 0.106 + 0.038 mm; 1% of pulp density; pH 4; 2%; and 12 days, respectively. The results demonstrated that the treatment with lignite-derived inocula removed 52% of total sulphur. After fungal desulphurization, organic sulphur and sulphate removal were obtained as 38% and 51%, respectively. (C) 2013 Elsevier Ltd. All rights reserved.