The sediment microbial communities of a disused coal mine lake, Lake Kepwari (pH~4.5-5) were studied to understand how the natural microbial processes in an oligotrophic acidic mine lake system influence the iron and sulphur cycles. Most probable number (MPN) viable counts were used to enumerate the benthic bacteria at different depths. MPN results revealed an abundance of bacteria that were capable of growing in sulphate reducing medium with numbers in the range of 1 × 107 – 1 × 108 cells.g-1 of wet sediment. In contrast, MPN results showed much lower numbers of bacteria that were capable of growing in ferric reducing medium with 1 × 102 – 2 × 103 cells.g-1 of wet sediment detected. Serial decimal dilution cultures were used to isolate pure strains of benthic bacteria. Strains HP1, HP2 and HP3 were isolated from benthic lake sediments at 18 m, 0 m and 10 m water depths respectively. 16S rRNA gene sequence analysis of strain HP1 showed that the strain belonged to the genus Enterobacter, strain HP2 belonged to the Order Rhizobiales and strain HP3 belonged to the sub-order Micrococcineae. Denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA gene fragments was used to profile the diversity of the benthic microbial communities at different depths. DGGE profiling of benthic sediments revealed that sediments contained mostly members of the Proteobacteria, Actinobacteria and Firmicutes phyla.