BACKGROUND: Barnyardgrass (Echinochloa spp.) is a global weed in rice fields. Quinclorac is commonly used to control barnyardgrass. However, due to persistent use, quinclorac resistance has evolved. We obtained quinclorac-susceptible (QS) and-resistant (QR1, QR2) lines from the progeny of a single resistant E. crus-pavonis for a resistance mechanism study. RESULTS: Line QR1 exhibited resistance to high quinclorac rates (up to 6400 g ha −1), whereas line QR2 exhibited a resistance/ susceptibility segregation ratio of 3:1 at the field or lower rates (400, 100 g ha −1). Intriguingly, a lower level of 14 C-quinclorac metabolism and hence a higher level of 14 C-quinclorac translocation was observed in QR1 than QS plants. The basal expression levels of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) and ACC oxidase 2 (ACO2) genes did not differ significantly between the QR1 and QS lines. However, more expression of ACS and ACO genes was induced by quinclorac treatment in QS than in QR1. Basal levels of ⊎-cyanoalanine synthase (⊎-CAS) gene expression were similar in QS and QR1 plants, but a greater level of down-regulation was detected in QS than in QR1 plants after quinclorac treatment. CONCLUSION: These results indicate QR plants are less responsive to quinclorac than QS plants in terms of up-regulating quinclorac metabolism and ethylene synthesis. Resistance in this E. crus-pavonis line is likely controlled by a single major gene, involving possibly an alteration in auxin signal perception/transduction to the ethylene biosynthesis pathway. The ⊎-CAS is unlikely to play a major role in quinclorac resistance in this particular population.