The cyanobacterium Synechocystis sp. strain PCC 6803 is one of the most important models for studying photosynthesis and ecology.Real-time fluorescent quantitative PCR and semi-quantitative PCR are extensively exploited to investigate the gene expression of this cyanobacterium. The quality of quantitative PCR template has a decisive influence on final data and the experimental results.When preparing Synechocystis sp. strain PCC 6803 RNA for quantitative PCR,degradation occurs frequently,leading to unreliable results.Methods for preparating quantitative PCR template from Synechocystis sp. strain PCC 6803 were improved.Results showed that the RNA isolated with the improved method was more intact and can be directly reverse-transcribed to the cDNA template for quantitative PCR.Using the cDNA template obtained,detecting genes with high expression can be performed simply by semi-quantitative PCR,while detection of those genes with low expression requires real-time fluorescent quantitative PCR.