The organic acids and polyphenols in apple (Malus ×domestica) juice are responsible for hard cider flavor, aroma, color, and microbial stability. The second chapter of this dissertation describes how the malic acid marker Ma1 was able to categorize 217 cider apple cultivars into low (<2.4 g·L-1), medium (2.4-5.8 g·L-1), and high (>5.8 g·L-1) acidity groups. Triploid cultivars had a significant 0.36 g·L-1 greater titratable acidity than diploid cultivars (P = 0.0111). The third and fourth chapters focused on the effect of crop density and early tree shading on polyphenol development in cider apples respectively to understand source-sink relationships and explain the year-to-year variation in polyphenol content. There was a significant increase in the concentrations of most polyphenol compounds, including monomeric and oligomeric proanthocyanidin compounds in the low crop density treatment (5 fruit/cm2 trunk cross-sectional area) compared to the unthinned control (P < 0.0100). Transcriptome profiling through RNA sequencing indicated the critical genes involved in hydroxylation, methylation, and glycosylation in the phenylpropanoid pathway were upregulated in the low crop density treatment at 27 DAFB and 81 DAFB, which corresponded with increased concentration of phenylpropanoids. Specifically, there was a significant increase in the expression of the gene encoding anthocyanidin reductase (catalyzes the production of epicatechin) in the low crop density treatment at 27 and 81 days after full bloom (P < 0.0100). In Chapter 4, carbohydrate stress applied through early tree shading (1-5 weeks after full bloom) reduced phenolic acids and quercetin glycoside concentrations at harvest in the 60-tree shade treatment (60% of photosynthetically active radiation blocked) in comparison to the unshaded control, with minimal impact on production of procyanidin monomers and oligomers in cider apples. Fruit shaded trees were not significantly different from the control. This dissertation elucidates a new marker-based acidity classification system allowing for cultivar comparisons across geographical, seasonal, and horticultural considerations; illustrates the differing polyphenol accumulation patterns in the peel and flesh tissue; provides compelling evidence for a positive source-sink relationship with polyphenol development in cider apples; and lists transcription factors that could possibly be involved in the polyphenol production in cider apples.