Olive (Olea europaea L.) is a typical crop species of the Mediterranean Basin. A number of cultivars were selected and propagated mainly vegetatively over the centuries for their qualitative and quantitative traits. Due to the long juvenile phase of the tree, few breeding programs have been performed. Therefore the most appropriate process is a selection scheme from heterogeneous populations or cultivars varying in oil quantity and quality, harvest regimes, and biotic and abiotic resistance. Molecular marker techniques have been applied recently on olive to relate, identify, distinguish and characterize different cultivars or genotypes and in order to provide information on olive origin and dispersal and to evaluate olive germplasm for traits with agronomical importance. To understand the regulation of biosynthetic pathways of oil and antioxidants on the molecular level, we have isolated a number of genes encoding for key enzymes in fatty acid and antioxidant biosynthesis, modification and triacylglycerol storage. The gene expression during fruit growth and seed development as well as their transient and temporal expression in different tissues is discussed in relation to storage of fatty acids and to provision of signaling molecules important in plant defense mechanisms and reproduction