A comparative study of the primary and secondary metabolites of the juice of several mandarin cultivars with different pollination, seed production and parthenocarpic abilities was carried out, and the antioxidant capacity of the hydrophilic fraction was measured. Correlation by a Principal Component Analysis and a Cluster Analysis was used. By a multivariate analysis, the 15 citrus cultivars were clustered into four groups consistently with citrus types. The presented data are an important factor for choosing varieties with high potential as a nutraceutical source. These aspects are necessary as consumers demand prevention of health problems through nutrition and certain fruit quality traits, including fruit size, internal quality, good rind color and easy peeling.