In GMO (genetically modified organism) detection process,PCR results are usually different among various laboratories. Non-specific amplification bands,primer-dimer and different detection sensitivity often occur. Taq DNA polymerase might be one of the reasons resulting in different PCR amplification. According to genetically modified rapeseed detection standard developed by Entry-exit Inspection Quarantine of P. R.China,18 Taq DNA polymerase were analyzed to amplify CaMV35S promoter in transgenic rapeseed OXY235. The results showed that Taq polymerase has severe impact on non-specific amplification and detection sensitivity. Hot-Start Taq polymerase was better for qualitative PCR detection,which produced clear target band in good sensitivity without non-specific amplification. However,it was found that,if Taq polymerase could not effectively amplify 0.1% DNA samples,it was not recommended in qualitative PCR detection.