BACKGROUND: Exploring the mechanisms of herbicide resistance in weeds is an important part of designing resistance management strategies and rationalizing herbicide use. Beckmannia syzigachne is one of the most important agricultural weeds in China. Long-term use of acetyl-CoA carboxylase (ACCase)-inhibiting herbicides has led to the evolution of herbicide resistance in B. syzigachne. ACCase-inhibiting herbicides comprise three chemical families: aryloxyphenoxypropionates (APPs), cyclohexanediones (CHDs) and phenylpyraxoline (DENs). RESULTS: Based on whole-plant dose–response experiments, a B. syzigachne population (BS-R) was confirmed to be 12- and 20-fold resistant to the APP herbicides quizalofop-P-ethyl and clodinafop-propargyl, and 2.2-, 2.8- and 2.8-fold resistant to fenoxaprop-P-ethyl, the CHD herbicide sethoxydim and the PPZ herbicide pinoxaden, respectively, compared with its susceptible counterpart (BS-S). Resistance to clodinafop-propargyl in the BS-R population could not be reversed by the known cytochrome P450 (CYP450) inhibitor malathion and the glutathione S-transferase (GST) inhibitor 4-chloro-7-nitrobenzoxadiazole. In addition, no difference in CYP450 and GST activity was confirmed between the BS-R and BS-S populations. ACCase gene sequencing revealed an Ile-2041-Val mutation in the BS-R population. A derived cleaved amplified polymorphic sequence marker was developed for rapid detection of the specific Ile-2041-Val mutation. Correlation quantification of resistance in homo- and hetero-resistant versus wild-type plants showed that resistance to clodinafop-propargyl in this population is conferred by the Ile-2041-Val mutation. CONCLUSION: Unlike previous reports on the unique cross-resistance pattern conferred by the 2041 mutation, this study demonstrates that the Ile-2041-Val mutation in BS-R population confers resistance to certain ACCase-inhibiting APP, CHD and PPZ herbicides in B. syzigachne.