This paper presents the results of DNA-based molecular analyses of the microbial community responsible for biological iron (Fe) and manganese (Mn) removal in slow sand filters (SSF). A lab-scale SSF was operated in 55-day sets under different operating conditions in order to evaluate long-term performance of the filter. The concentrations of Fe and Mn in synthetic feed water were increased from 1 mg/L to 2 mg/L at two different filtration rates (0.1 and 0.3 m/h). Daily samples were taken from influent and effluent for turbidity and Fe-Mn concentration measurements. 90-95% removal efficiencies were achieved with very low effluent concentrations. PCR-DGGE analyses were performed on samples, and Gallionella, Leptothrix, Crenothrix, and Hyphomicrobium were identified as the main microbial strains responsible for iron and manganese oxidation in SSF. Results also revealed that microbial activity was the main mechanism for Fe and Mn removal in the early stages of operation.