This study was assessed such that a molecular biological investigation in uncontrolled landfills can be comparably used for characterizing its stability in association with the conventional water quality parameters. At first, the microbiological diversity in two landfill sites (Cheonan and Wonju landfills in Korea) was identified by 16s rDNA cloning. It was also quantitatively investigated for denitrification enzyme coding genes (nitrite reductase; nirS and nitric oxide reductase; cnorB) and methane producing enzyme coding gene (methyl coenzyme M reductase; MCR) by realtime polymerase chain reaction. The copy numbers of nirS and cnorB in Cheonan were higher than those in Wonju, which was well reflected from the time difference after site closure, respectively. The greatest number of MCR, nirS and cnorB genes of C1 spot (Cheonan) verified that it was immediately bordering the sources, which was steeply decreased toward the outer boundary landfill. Cheonan landfill is more rapidly stabilized based on molecular biological indicator even if the present state of Wonju landfill is more stable based on BOD and COD concentrations. However, the comparison between the copy number of these genes and the conventional water quality monitoring parameters addressed that those of parameters have similar patterns, especially for the source or the boundary. It was concluded that the molecular biological parameters could be used for determining microbial stability toward down-gradient around the uncontrolled sites.