Herbicide resistance is an evolutionary process that affects entire agricultural regions' yield and productivity. The high number of farms and the diversity of weed management can generate hot selection spots along regions. Resistant biotypes can present a diversity of mechanisms of resistance and resistance factors depending on selective conditions inside the farm; this situation is similar to predicts by the geographic mosaic theory of coevolution. In Mexico, the agricultural region of Bajio has been affected by herbicide resistance for 25 years. To date, Avena fatua L. is one of the most abundant and problematic weed species. The objective of this study was to determine the mechanism of resistance of biotypes with failures in the weed control in 70 wheat and barley crop fields in Bajio, Mexico. The results showed that 70% of farms have biotypes with TSR, the most common mutations where Trp – 1999 – Cys, Asp – 2078 – Gly, Ile – 2041 – Asn, such mutations confer cross-resistance to ACCase-inhibiting herbicides. Metabolomic fingerprinting showed four different metabolic expression patterns. The results confirmed that in the Bajio exist multiple selection sites for both resistance mechanisms, which proves that this area can be considered as a geographic mosaic of resistance.