Abstract: To examine the spatial changes of microbial community in an iron mine of the upstream area of Miyun Reservoir, soil samples were collected from twelve sites. Quantification of bacteria, fungi and actinobacteria were determined by real-time PCR. Derived from Pearson correlation analysis showed that there was significant positive correlation (P<0.05) between the abundance of total microbes and w(AP). Meanwhile, the abundance of bacteria and actinobacteria had significant negative correlation with contamination index(R=-0.756, P<0.01; R=-0.614, P<0.05). Pollution levels, however, had no effect on fungi abundance. PCR-DGGE was used to analyze the bacteria, fungi, and actinobacteria community structure as well. Redundancy analysis demonstrated that contamination index greatly influenced on bacteria and actinobacteria community (P<0.05) and less influenced on fungi. The diversity of bacteria and actinobacteria increased from low to moderate levels of contamination and then decreased at relatively high contamination index. The changes of microbial abundance and structure revealed that different microbial communities exhibit various responses to heavy metals. Fungi were the most tolerated species to heavy metals, followed by actinobacteria and bacteria in the same contaminant grade. Moreover, Cr, Pb and Zn promoted the abundance and the diversity of microbial community in their moderate pollution. The distribution of microbial community, however, was inhibited by Cd and Cu. This indicated that microbial communities would shift from sensitive population to tolerant population, and it was important to further understand their synergic relationship and biogeochemical processes.