Abstract: The circadian rhythm in cyanobacterium Synechococcus elongatus PCC 7942,which is driven by a central oscillator consisted of KaiA,KaiB and KaiC protein,is considered to be the simplest model to explain the endogenous time keeping mechanism in prokaryotic cells.To make a better understanding of how the clock genes are arranged together in this cyanobacterium,it's important to study the expression patterns of these clock genes under entrained conditions.Due to the complex cell wall structure of S.elongatus PCC 7942,which makes getting high quality and high quantity RNA quite difficult,there are quite few reports on the studies of the expression patterns of the clock genes via qPCR method.In the present study,an optimized qPCR system to S.elongatus PCC 7942 cells was established by optimizing the key factors which affected the efficiency and accuracy of qPCR,such as the initial cells amount for RNA isolation,the lysozyme digestion time of the cell walls,the removal method of genomic DNA,the purification method of cDNA templates,as well as the concentration of the primers and annealing temperature of PCR,etc.The results indicated that 10mL cyanobacterial cells with OD750≈0.4(about 1.1mg in dry weight) treated by 3mg/mL lysozyme for 10mins,were the best for total RNA isolation by a RNA extraction Kit;The process of removing the residual genomic DNA from the total RNA by DNase1 before being applied as templates for cDNA synthesis,and the purification of cDNA by a universal DNA recovery kit after reverse transcription reaction would significantly promote the quantity and repeatability of following qPCR.It is conclude that adjusting cDNA template concentration to 0.1μg/μL and primers concentration to 4 pmol/L,while performing the real-time qPCR under the optimized annealing temperatures on the basis of semi-quantity RT-PCR play a pivotal role in analyzing the clock genes expression profiles in cyanobacterium S.elongatus PCC 7942 by qPCR.