The production of anthocyanins in fruit tissues is highly controlled at the developmental level. We have studied the expression of flavonoid biosynthesis genes during the development of bilberry (Vaccinium myrtillus) fruit in relation to the accumulation of anthocyanins, proanthocyanidins, and flavonols in wild berries and in color mutants of bilberry. The cDNA fragments of five genes from the flavonoid pathway, phenylalanine ammonia-lyase, chalcone synthase, flavanone 3-hydroxylase, dihydroflavonol 4-reductase, and anthocyanidin synthase, were isolated from bilberry using the polymerase chain reaction technique, sequenced, and labeled with a digoxigenin-dUTP label. These homologous probes were used for determining the expression of the flavonoid pathway genes in bilberries. The contents of anthocyanins, proanthocyanidins, and flavonols in ripening bilberries were analyzed with high-performance liquid chromatography-diode array detector and were identified using a mass spectrometry interface. Our results demonstrate a correlation between anthocyanin accumulation and expression of the flavonoid pathway genes during the ripening of berries. At the early stages of berry development, procyanidins and quercetin were the major flavonoids, but the levels decreased dramatically during the progress of ripening. During the later stages of ripening, the content of anthocyanins increased strongly and they were the major flavonoids in the ripe berry. The expression of flavonoid pathway genes in the color mutants of bilberry was reduced. A connection between flavonol and anthocyanin synthesis in bilberry was detected in this study and also in previous data collected from flavonol and anthocyanin analyses from other fruits. In accordance with this, models for the connection between flavonol and anthocyanin syntheses in fruit tissues are presented.Fruit development from flower to ripe fruit is a complex process that involves modification of cellular compartments, loss of cell wall structure causing softening, and accumulation of carbohydrates (Brady, 1987). The production of secondary metabolites during the ripening process is an essential phenomenon for the contribution of seed dispersal of the plant in the form of accumulation of pigments and flavor compounds. The significance of secondary products in defense against diseases in developing fruits should also be remembered (Harborne, 1997;Mercier, 1997).Flavonoids are a large group of phenolic secondary metabolites that are widespread among plants and are involved in many plant functions. Anthocyanins, a flavonoid subclass, are the main pigments in flowers and fruits, acting as insect and animal attractants (Bohm, 1998;Harborne and Williams, 2000). Anthocyanins are synthesized via the phenylpropanoid pathway (Fig. 1). Anthocyanin biosynthesis has been extensively studied in several plant species, and, therefore, detailed information of the course of reactions is available. Two classes of genes are required for anthocyanin biosynthesis, the structural genes encoding the enzymes...