Mutations in chloroplastic acetyl-CoA carboxylase (ACCase) gene enables molecular tools such as allele-specific PCR assay to monitor resistance alleles in green algae (Chlorophyta) Scenedesmus quadricauda. An isoleucine-leucine substitution in the gene encoding chloroplast (ACCase) conferred resistance to clodinafop-propargyl herbicide. Green algae cultures were treated with different concentrations of this herbicide (0, 1/16, 1/8, 1/4, 1/2, 1 and double of field concentration). The free amino acid content and cell number were determined after 0, 24, 48, 72 and 96 hrs. Concerning cell number, from  the first to third generation, the number of cells decreased especially in the highest two concentrations. From the fourth to sixth generation the number of cells increased in all tested concentrations except the two highest concentrations. With regard to amino acid content, results indicated that from the first to sixth generation an increase occurred in amino acid content 24 hrs after exposure and decreased 48-96 hrs after exposure. In the fourth and fifth generation amino acid content increased, while in the sixth generation decreased. That might be explained by the recovery of algae activity at the sublethal concentrations, emergence of algae resistant population as well as increase in algae cell number. The results of allele-specific PCR revealed the presenence of (C) allele in algal cultures which explain the resistance to the herbicide used.