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Apple scab, caused by <i>Venturia inaequalis</i>, is an economically devastating disease of apple in the northeastern United States. The proliferation of resistance to DMI fungicides, combined with the limited release of novel chemistries with high levels of activity against apple scab has led to a greater reliance on QoI fungicides. Current techniques used to screen for QoI resistance in <i>V. inaequalis</i> provide only a qualitative analysis and fail to account for the heteroplasmic nature of the mitochondrial cytochrome B (<i>CYTB</i>) gene, the target site of QoI fungicides. To identify emerging QoI resistance in apple scab populations we quantified sensitive and resistant alleles in 31 monoconidial <i>V. inaequalis</i> isolates collected from 14 orchards in the northeastern US. Allele-specific PCR primers were designed to detect and quantify the relative abundance of the resistant A143 allele using allele-specific qPCR. The percentage of resistant alleles in monoconidial <i>V. inaequalis</i> isolates ranged from 0-100%. Isolates devoid of the resistant allele had % relative growth (%RG) values on trifloxystrobin-amended media ranging from 0-45%, while isolates in which only A143 was detected ranged from 81-135% RG. Nearly one third of isolates screened demonstrated heterogeneity of the <i>CYTB</i> gene having both resistant and sensitive alleles. For populations composed of such isolates, QoIs may still provide a high level of efficacy following application curtailment. <p><p>Keywords: Fungus, Fruits-Nuts, Apple