The copper, iron and sulfur speciation of chalcopyrite leached by moderate thermophile Sulfobacillus thermosulfidooxidans was investigated by combining synchrotron radiation X-ray diffraction (SR-XRD) and X-ray absorption near edge structure (XANES) spectroscopy. Leaching experiment showed that the leaching rate of copper was 73.6% after 20 days bioleaching. Results of scanning electron microscopy of leaching residues showed that the surface of chalcopyrite was gradually corroded. Results of SR-XRD showed that orthorhombic form alpha-S-8, jarosite and chalcocite were produced at day 4; the bioleaching residue contained jarosite, covellite and alpha-S-8 besides chalcopyrite from day 8. The Cu, Fe and S K-edge XANES spectra quantitatively analyzed the copper, iron and sulfur species compositions of leaching residues, and the fitted results showed similar trend to SR-XRD results. According to both SR-XRD and XANES study, bornite and amorphous elemental sulfur mu-S were not found during bioleaching of chalcopyrite by S. thermosulfidooxidans. By conclusion, it indicated that iron-deficiency sulfide chalcocite first formed at the initiation of bioleaching with a low Eh value, and it then gradually transformed to covellite at a high Eh value. Meanwhile, alpha-S-8 and jarosite were produced as the predominant intermediates. By combining SR-XRD and XANES, it was useful for better understanding the dissolution mechanism of chalcopyrite during bioleaching by qualitatively and quantitatively analyzing in situ the surface chemical composition of the minerals. (C) 2015 Elsevier B.V. All rights reserved.