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This paper studied the structure and dynamic change of microbial communities in bio-reactor for treating ground water which contained high concentration of iron and manganese.In this study, polymerase chain reaction (PCR) denaturing gradient gel electrophoresis (DGGE) was used to evaluate the bacterial diversity.Different samples in spatio-temporal of bacterial community suceession in sands were analyzed, and the removal of iron and manganese were .discussed.The results showed that a significant change in the community structure was observed during running time and the bio-reactor which designed by ourselves: the removal rate of iron and manganese could achieve 88.93%.The mass of microrganisms was decreasing, and the type of micro-organisms tended to stable with the increase of operating time.Besides, the change of mass and types of micro-organisms in sands was related to temperature.Along the depth of filter layer, the mass and types of micro-organisms were gradually decreasing.Further, pseudomonas were found to be the main microbiology by recycling the band sequencing and phylogenetic analysis.And with time increasing the mass and kind of bacteria were growing from less to more, finally to be stable.