This paper describes about microbial diversity in an iron oxidation tank of an AMD treatment plant established at an abandoned sulphur mine in Japan. Since the mining operation was stopped, this mine has produced strong acidic mine drainage, pH 1.8, including a high concentration of ferrous iron, 301mg/L, and the flow rate was about 4m3/min. In 2006, a pilot scale microbial iron oxidizing system was installed to remove total iron more easily from the AMD by oxidizing ferrous iron to ferric iron. From the start of this pilot operation, microbial diversity in the iron oxidation tank was investigated using a PCR-DGGE method for about two months. In the PCR, V3 region of 16S rRNA gene for Bacteria was amplified. The profiles of DGGE showed that there were three dominant species in the iron oxidation tank through the experimental period. Number of bands on DGGE profiles decreased with dates of sampling so that the microbial population became less diverse because of the iron oxidizing operation. There was a wide variety of bacterial species of even though conditions were strongly acidic.