AbstractArbuscular mycorrhizal fungi (AMF) protect host plants against diverse biotic and abiotic stresses and promote biodegradation of various contaminants. In this study effect of Glomus mosseae/Medicago sativa mycorrhiza on atrazine degradation was investigated. It was observed that the atrazine degradation rates with any addition level in mycorrhizal treatments were all significantly higher than those in non- mycorrhizal treatments. When atrazine was applied at 20 mg kg−1, the removal efficiency was up to 74.65%. Therefore, G. mosseae can be considered as ideal inhabitants of technical installations to facilitate phytoremediation. Furthermore, a total of 10.4 Gb was used for de novo transcriptome assembly, resulting in a comprehensive data set for the identification of genes corresponding to atrazine stress in the AM association. After comparative analysis with edgeR, a total of 2,060 differential expressed genes were identified, including 570 up-regulated genes and 1490 down-regulated genes. After excluding ‘function unknown’ and ‘general function predictions only’ genes, 172 up-regulated genes were obtained. The differentially expressed genes in AM association with and without atrazine stress were associated with molecular processes/other proteins, zinc finger protein, intracellular/extracellular enzymes, structural proteins, anti-stress/anti-disease protein, electron transport-related protein and plant growth associated protein. Our results not only prove AMF has important ecological significance on atrazine degradation but also provide evidence for the molecular mechanisms of atrazine degradation by AMF.