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The organic acid concentration in apple (Malus ×domestica) juice is a major component of hard cider flavor. The goal of this study was to determine if the malic acid markers, Ma1 and Q8, could classify the titratable acidity concentration in cider apple accessions from the United States Department of Agriculture Malus germplasm collection into descriptive classifications. Our results indicate that for diploid genotypes, the Ma1 marker alone and the Ma1 and Q8 markers analyzed together could be used to predict cider apple acidity (P < 0.0001). Alone, the Ma1 marker categorized acidity into low (−1), medium (2.4–5.8 g⋅L−1), and high (>5.8 g⋅L−1) groups. The combination of Ma1 and Q8 markers provided more specificity, which would be useful for plant breeding applications. This work also identified a significant difference (P = 0.0132) in acidity associated with ploidy. On average, the triploids accessions had 0.33 g⋅L−1 higher titratable acidity than the diploid accessions. Based on the results of this work, we propose a genetics-based classification system for cider apples with the acidity component defined by the Ma1 and Q8 markers.