Vertical changes in archaeal community structure in mesophilic freshwater lake sediment were investigated using denaturing gradient gel electrophoresis of amplified 16S rRNA genes and reversely transcribed 16S rRNA fragments. Electrophoretic band pattern of archaeal community did not drastically change with depth. The archaeal 16S rRNA-based denaturing gradient gel electrophoresis band pattern was very similar to the 16S rDNA-based pattern. These results indicate that archaeal community structure does not drastically change throughout the 0-20 cm in depth, and most archaeal populations in the sediment retain extractable rRNA. Phylogenetic analysis of seven sequences retrieved from both DNA- and RNA-based denaturing gradient gel electrophoresis revealed that these sequences were divided into four major lineages; the kingdom Crenarchaeota, the order Methanomicrobiales, the family Methanosaetaceae, and an uncultured cluster within Euryarchaeota. The order Methanomicrobiales and the family Methanosaetaceae were the dominant methane-producing archaea in this profundal freshwater lake sediment. Moreover, we found Euryarchaeota that are not related to methanogens, and non-thermophilic Crenarchaeota. This suggests that archaeal populations other than methanogens in low-temperature sediment have been previously underestimated.