Antioxidants, antioxidant capacity, and the expression of isoprenoid metabolism–related genes and two pigmentation-related transcription factors were studied in four native and four hybrid tomato (Solanum lycopersicum) genotypes with different-colored fruit. Red fruit genotypes were associated with greater lycopene, β-carotene, lipophilic antioxidant capacity, and greater chromoplast-specific lycopene β-cyclase (CYC-B) transcript levels. Orange fruit genotypes had greater concentrations of tocopherols and greater transcript levels of homogentisate phytyl transferase (VTE-2), 1-deoxy-D-xylulose phosphate synthase (DXS), and 4-hydroxyphenylpyruvate dioxygenase (HPPD). The yellow fruit genotype was greater in total polyphenol and hydrophilic antioxidant capacity with greater expression of geranylgeranyl reductase (GGDR), phytol kinase (VTE-5), phytoene synthase (PSY) 2, lycopene β-cyclase (LCY-B), SlNAC1, and SINAC4. Greater levels of individual antioxidants were associated with specific coloration of tomato fruit. Moreover, the negative correlations between the expression of PSY1 and VTE-5, and between lycopene and chlorophyll, suggest a balance between carotenoids, tocopherols, and chlorophylls. The results of this study support either the direct commercialization of tomatoes with different color fruit or use of their genotypes in breeding programs to increase antioxidant levels among existing cultivars.