The microbial ecology of the bioleaching of Ni-Cu sulfide is poorly understood and little effort has been made to handle the microbiological components of these processes. In this study, denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rRNA genes fragments from bacteria was used to evaluate the changes of the bacterial community in the process of Ni-Cu sulfide bioleaching in a shaken flask system. The results revealed that the bacterial community was disturbed after the addition of Ni-Cu sulfide. Phylogenetic analyses of 16S rRNA fragments revealed that the retrieved sequences clustered together with the genera Acidithiobacillus and Leptospirillum. Multidimensional scaling (MDS) and cluster analysis of DGGE-banding patterns revealed that the process of Ni-Cu sulfide bioleaching in 46 days was divided into three stages. During the bioleaching process of Ni-Cu sulfide, Leptospirillum was always dominant. The genera Acidithiobacillus was only detected at early and later stages of the bioleaching process. These results extend our knowledge on microbial dynamics in Ni-Cu sulfide bioleaching, a key issue required to improve commercial applications. (C) 2010 Elsevier Ltd. All rights reserved.