Fruits are rich sources of antioxidants including flavonoid polyphenolic compounds. This flavonoid content plays crucial roles in fruit pigmentation and seems to be associated with favourable health-effects due to their free radical scavenging activity. Commonalities and differences are well-known in the flavonoid contents of different fruit crops, which suggest alterations in the flavonoid biosynthesis pathway of fruit tissues. The amounts of water-soluble polyphenolic compounds in fruit may also differ according to various genotypes of the same species. Many efforts have been taken in the last few years to understand the flavonoid biosynthesis pathway in fruits including pomes, berries, citrus and stone fruits. We examined the flavonoid biosynthesis in two different apricot (Prunus armeniaca L.) genotypes characterized by markedly different total antioxidant capacities and polyphenolic contents. The hybrid 'Preventa' with outstanding polyphenolic content was compared with the traditional Hungarian cultivar 'Gönci magyarkajszi'. Degenerate primers were designed based on gene sequences from closely related species and a homology based approach was used to identify flavonoid genes in P. armeniaca. We were successful in determining partial cDNA sequences of some genes encoding the key enzymes in the phenylpropanoid and flavonoid biosynthesis pathways including phenylalanine ammonia-lyase, cinnamate-4-hydroxylase, chalcone synthase, chalcone isomerase, flavanone 3- hydroxylase, flavonoid 3'-hydroxylase, flavonol synthase, dihydroflavonol 4- reductase, anthocyanidin synthase, anthocyanidin reductase, leucoanthocyanidin reductase and UDP glucose:flavonoid 3-O-glucosyltransferase. The availability of such novel apricot gene sequences made quantitative real-time PCR (qRT-PCR) analyses possible. We determined transcript levels of the genes encoding the identified enzymes. By comparing gene expression profiles of the tested apricot genotypes with different polyphenolic contents, enzymes responsible for the metabolomic differences were identified. The qRT-PCR analysis was optimized for expression analysis through different ripening stages, which helped to identify the fruit developmental stages having crucial influence in forming the antioxidant capacity and composition of fruit tissues.