We have investigated a correlation of transcript abundances of key genes that influence the quality of wood and flavonoid biosynthesis, such as the two p-hydroxycinnamoyl-CoA:quinate shikimate p-hydroxycinnamoyl transferase (HCT) and the two chalcone synthases (CHS) from Eucalyptus globulus grown in a greenhouse. The EglHCT1 and EglHCT2 transcripts accumulated in stems of all ages, but to a lesser extent in leaves. On the other hand, EglCHS3 and EglCHS4 exhibited high transcript levels in leaves, roots and shoots, but low levels in the stem. A positive correlation (R² > 0.70) was observed between the transcript levels of the EglHCT1, EglHCT2 genes and Klason lignin (KL) content. In addition, the sum of transcript levels of EglHCT1 and EglHCT2 genes were highly correlated to KL contents (R² > 0.85). However, there is no relationship between transcript levels of two CHS genes and, KL or flavonoid contents. This may imply that lignin biosynthesis and flavonoid biosynthesis are independently regulated in E. globulus.