Abstract: The biological activity and bacterial community composition in biologically aerated filter( BAF) with zeolite and ceramic medium for treating source water at low temperature were investigated by oxygen uptake rate and polymerase chain reaction-denaturing gradient gel electrophoresis combined with cloning and sequencing. Results showed that the removals of the ammonia nitrogen and the permanganate index slightly decreased with the decrease of temperature in both zeolite and ceramic BAFs. Even so,the removals in two BAFs still showed a satisfactory performance. The main removals of ammonia nitrogen and permanganate index in two BAFs were performed below 40 cm and 55 cm height,respectively. Low temperature had a significant effect on biological activity of two BAFs,especially for heterotrophic bacterium. During the whole operation,the biodiversity was enriched in two BAFs. It was no significant difference of dominant species between the low and room temperature. The changes of dominant species were obvious when the temperature became lower. The Nitrosospira was enriched and became thedominant species,while the Nitrospira disappeared in initial stage. In addition,the dominant species in two BAFs were similar after a long-term operation at low temperature.