AbstractBACKGROUNDBiotypes of Avena fatua resistant to ACCase‐inhibiting herbicides have been reported in the States of Baja California (BC) and Sonora (SON), Mexico. We hypothesised that resistant biotypes present in SON (Valle de Hermosillo and Valle del Yaqui) are derived from a resistant population from BC (Valle de Mexicali) via gene flow through the transport and exchange of contaminated wheat seed. This study aimed to determine (1) the resistance of A. fatua to ACCase‐inhibiting herbicides in populations from BC and SON, (2) the mutation at the site of action and (3) the genetic structure and gene flow among populations.RESULTSDNA sequencing showed that all biotypes shared the same mutation (Leu × Ile at codon 1781). Microsatellites showed evidence of a genetic bottleneck in SON, and spatial analysis of molecular variance grouped one biotype from the Valle de Mexicali with two biotypes from the Valle de Hermosillo. Migration analysis suggested gene flow from the Valle de Mexicali to the Valle de Hermosillo, but not to the Valle del Yaqui.CONCLUSIONSThe presence of resistant biotypes of A. fatua in the Valle de Hermosillo, SON, are likely derived from seeds from BC, possibly through the transport of contaminated wheat seeds. © 2016 Society of Chemical Industry