Abstract: Among the aquatic organisms,algae are one of the most susceptible organisms to pollution in water.Transcriptional abundance has been gradually used as a surrogate for gene expression in environmental biology.In the present study,real-time PCR assay was established to quantify the transcript abundances of three photosystem genes(psaB,psbC and rbcL) in Chlorella vulgaris,and the acute toxicity of three herbicides(glufosinate,atrazine and diclofop-methyl) was assessed using this method.The results demonstrated that real-time PCR is an efficient technique to assess the toxicity of xenobiotic compounds in aquatic system.