Eggplant is a widely consumed vegetable, with significant nutritional value and high antioxidant content, mainly due to its phenolic constituents. Our goal was to determine the levels of carbohydrates, proteins, total phenolics, anthocyanins, flavonoids, chlorogenic acid, and the antioxidant capacity in thirteen eggplant cultivars cultivated in Greece and to identify sequence polymorphisms in key regulating genes of the phenylpropanoid pathway (C4H, HCT, HQT, C3H, F3H, ANS, MYB1), which might relate to the phytochemical content of those cultivars. The carbohydrates’ content differs among and within cultivars, while the rest of the phytochemicals differ only among cultivars. The cultivars ‘EMI’ and ’Lagkada’ scored higher than the rest in phenolics, anthocyanins, ascorbic acid, caffeoylquinic acid, and antioxidant capacity. Moreover, significant correlations were observed between various ingredients and the antioxidant capacity (FRAP and DPPH). Sequence analysis revealed several SNPs in C4H, HQT, F3H, ANS, and MYB1 among the cultivars studied. According to chi-square and logistic regression analyses, the missense mutation C4H4-108 correlates significantly with flavonoids, anthocyanins, and proteins; the synonymous mutation HQT-105 correlates with anthocyanins and ascorbic acid; the missense mutation HQT-438 correlates with flavonoids and chlorogenic acid, while the missense mutation ANS1-65 correlates with anthocyanins and sugars. These polymorphisms can be potentially utilized as molecular markers in eggplant breeding, while our data also contribute to the study of eggplant’s secondary metabolism and antioxidant properties.