The ascomycete Sphaeropsis sapinea (syn. Diplodia pinea), the causal agent of Diplodia blight of pine, is also known to be an endophyte with a latent pathogenic potential on pine trees. Due to climate change effects, especially warming and more prolonged or frequent drought events, the hosts are weakened and S. sapinea could become more aggressive in the future. Normally, pines which are 25years old or older are more susceptible to the disease as compared with younger trees. However, if younger trees are growing on poor sites or are located close to affected trees, they may also become infected. Here, we analyzed the interaction of young pine seedlings (4years old) with the fungus in vitro, in order to examine the changes in gene activity for example of genes encoding metabolites and therewith contributing to an induced resistance against the fungus. During different stages of infection (control without infection and 14days after infection), pine needles of four samples per stage (eight samples all together) were collected and analyzed by mRNA sequencing. The comparison between the two stages showed that, nearly independent of the genotype of the plant, 5691 genes were differentially expressed. In the severe stage of infection, elevated transcript levels of genes involved in lignin- and phytoalexin-biosynthesis and of pathogenesis-related genes were found. Furthermore, some of these genes were also validated in a natural population of Pinus sylvestris by reverse transcriptase (RT)-PCR in order to analyze induced defense responses.