Cercospora leaf spot (CLS) is the most damaging foliar disease of sugar beet globally. To combat CLS, multifaceted efforts are widely employed, including breeding for resistance, cultural practices, and the application of fungicides. However, populations of Cercospora beticola have become resistant to most fungicides used for CLS management, including those in the sterol demethylation inhibitor (DMI) class of fungicides. In this study, we sampled nearly 600 isolates of Cercospora beticola from MN and ND during the 2021 sugar beet growing season. For each isolate, EC50 values were determined for DMIs tetraconazole (Eminent), prothioconazole (Proline), difenoconazole (Inspire), and mefentrifluconazole (Revysol). Using the CYP51 gene sequence for each isolate, we determined that the synonymous E170 mutation and the synonymous/nonsynonymous L144(F) can be used to predict resistance to these four DMIs. The prevalence and accuracy of the six mutation combinations were calculated and specific combinations can predict resistance with greater than 90% accuracy. Interestingly, one prevalent mutation combination resulted identified cross-resistance to difenoconazole and mefentrifluconazole, but sensitivity to tetraconazole and prothioconazole. This data reveals the importance of codon bias in fungicide resistance and is the first demonstration of the use of synonymous mutations to predict cross-resistance.