In this study, long term nitrification performances and microbial composition in a full-scale oxidation ditch type wastewater treatment plant (WWTP) were monitored and evaluated using different molecular methods; fluorescent in situ hybridization (FISH), slot-blot hybridization and quantitative real-time polymerase chain reaction (PCR) method. In situ and membrane hybridization results indicated that Nitrosomonas species were identified as the dominant ammonia oxidizing bacteria and Nitrospira related species were detected as the prevailing nitrite oxidizing bacteria in a full-scale wastewater treatment plant throughout 2 years of operation. Real-time PCR using the LightCyclerinstrument has been developed for the quantification of ammonia monooxygenase (amoA) and 16S rRNA genes. Results suggest that real-time PCR analysis, amoA/16S rRNA ratio, is an alternative method to understand nitrifying bacterial population and activity in wastewater treatment plant compared with the FISH and slot-blot hybridization assays. The autotrophic/heterotrophic bacterial ratio and their influence on reactor performances were investigated using real-time PCR amoA/16S rRNA gene copy ratios and the results showed that this ratio varied from 3.6% to 8.3% during operational period.