SummaryPhenolic compounds are essential components of the defensive chemical arsenal of conifer trees. This chemically diverse group encompasses stilbenoids, flavonoids, isoflavonoids, proanthocyanidins and lignans. All of them are produced from the common precursors, CoA esters of the phenylpropanoids: p‐coumaroyl‐CoA, cinnamoyl‐CoA, caffeoyl‐CoA and feruloyl‐CoA. Two classes of enzymes, stilbene synthases and chalcone synthases, play important roles in the biosynthesis of plant phenolics, such as the conversion of the phenylpropanoid‐CoA esters into stilbenoids and flavonoids, respectively. In this study, we investigated the transcriptional responses of the Scots pine (Pinus sylvestris) genes encoding stilbene and chalcone synthases to the infection by the fungal pathogen Heterobasidion annosum. The experiments were performed on pine seedlings and mature trees. Our results show that the stilbene synthase gene is strongly induced in both age groups, but the level of induction in adult trees varied considerably among individual trees. Systemic induction in needles and hypocotyl regions was documented in young seedlings following fungal inoculation in root region. Concurrent changes in the expression of the chalcone synthase gene in response to fungal infection were much less pronounced. Our data confirm previous observations on the differential regulation of these enzymes in Scots pine and emphasize the role of stilbene synthase in the induced response to fungal infection.