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This study investigated the removal of selenite from wastewater using the fungus Asergillus niger KP isolated from a laboratory scale inverse fluidized bed bioreactor. The effect of different carbon sources and initial selenite concentration on fungal growth, pellet formation and selenite removal was first examined in a batch system. The fungal strain showed a maximum selenite removal efficiency of 86% in the batch system. Analysis of the fungal pellets by field-emission scanning electron microscopy, field-emission transmission electron microscopy and energy-dispersive X-ray spectroscopy revealed the formation of spherical-shaped elemental selenium nanoparticles of size 65–100 nm. An increase in the initial selenite concentration in the media resulted in compact pellets with smooth hyphae structure, whereas the fungal pellets contained hair like hyphae structure when grown in the absence of selenite. Besides …