In this study, the removal and reduction of selenite [Se(IV)] by growing Aspergillus sp. J2 were investigated. The lag phase, growth rate and biomass of J2 was not significantly influenced by the presence of 100 mg/L Se(IV). A rapid Se(IV) removal process took place from the 3rd to the 4th day during the growth of J2. Scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy and X-ray diffraction analyses showed that the Se(IV) did not cause any visible effects on cell morphology and the reduced amorphous elemental selenium [Se(0)] nanoparticles were mainly on the surface of the mycelial cell walls. The macromolecules containing amine groups also interact with Se(IV) and could play an important role in Se(IV) removal by J2.