Fruits are consumed not just for their taste but also their nutritional value. The major primary metabolites in fruit are sugars and acids, whose contents change during fruit growth and determine ultimate fruit quality. Fruits are also a source of antioxidant metabolites, which are important to human health due to their role in reducing risk of cancer and cardiovascular diseases. Antioxidants are equally important in the plant as they help fight against oxidative stress. Here we investigated the consequences of changes in the primary metabolism in acidic and acidless citrus genotypes during the major stages of fruit growth on the expression of antioxidant enzymes and the markers of cellular oxidation (hydrogen peroxide, malondialdehyde) in acidless (Iaffaoui orange and sweet lemon) and acidic (Salustiana orange and Villafranca lemon) citrus fruits. Glucose and fructose were the major sugars in the acidless lemon. Sucrose was the major sugar in the acidic lemon. Oranges shared a balance of glucose, fructose and sucrose. Malic and citric acid concentrations were higher in acidic lemons than acidless fruits. Acidic genotypes had higher hydrogen peroxide concentrations than acidless genotypes, whereas MDA concentrations were higher in oranges than in lemons. Specific activities of ascorbate peroxidase, catalase, superoxide dismutase and dehydroascorbate reductase were on the whole higher in acidic than acidless fruits. Principal component analysis revealed between-genotype divergence in antioxidant system, giving three groups: acidic lemons, acidless lemons, and oranges.