The study on arsenopyrite and realgar of bacterial oxidation shows that the chemical behaviors of different arsenic-bearing sulphides oxidated by thermophilic bacteria are quite distinct. Arsenopyrite is active and quickly eroded in bacteria-bearing solution. With a high leaching rate over 95%, the arsenopyrite phase cannot be detected by X-ray diffraction(XRD). Arsenopyrite is highly toxic to bacteria that at the initial stage of bio-oxidation, bacterial growth is inhibited and the number of bacterium cell drops from 2.26 × 108/mL to the lowest 2.01 × 105/mL. At the later stages of bio-oxidation, bacteria grow fast and reach 2.23 × 108/mL. Comparably, realgar is inertial and resistive to bacterial corrosion and oxidation. Arsenic in realgar crystal is hard to be leached and the residue is still realgar phase, as indicated by XRD. The cell number of bacteria varies a little, decreasing from 2.26 × 108/mL to 2.01 × 107/mL, during the bacterial oxidation. The results show that the crystal structure and arsenic valency of arsenic-bearing sulphides play a vital role during the leaching process of bacterial oxidation.