Expression profiles of four genes of the phenylpropanoid pathway (PAL, CCR1, HCT1, and CAD) as well as the peroxidase PaPX3 and the class IV chitinase PaCHI4, with α-Tubulin used as control, were investigated in bark and sapwood of Picea sitchensis clones showing similar susceptibility after 3-days wounding and artificial inoculation with Heterobasidion annosum sensu stricto. Constitutive levels were compared with levels induced after treatment at two locations (the site of inoculation and a distal zone, 1 cm away from inoculation site) to determine if they would differ in a fungal treatment as compared to wounding only. In addition, lignin and soluble and cell wall bound phenolics were extracted from the distal zone only, after inoculation. Compared to constitutive levels, different metabolic processes occurred in bark and sapwood: after treatment, in bark all genes were up-regulated, whereas in sapwood all genes except for PaPX3 and PaCHI4 were down-regulated. In bark all genes except for CAD had greater levels at the site of inoculation than in the distal zone, whereas in sapwood PAL, CCR1, HCT1, and CAD had lower levels at the site of inoculation than in the distal zone. Furthermore, compared to wounding only, inoculation with H. annosum triggered significantly different CAD, PaPX3, and PaCHI4 levels in bark but not in sapwood. Different amounts of lignin and soluble and cell wall bound phenolics were found in bark and sapwood. In bark, wounding and inoculation triggered significantly different cell wall bound phenolics (unknown2, unknown3, coniferin, astringin, taxifolin, piceid, and isorhapontin) compared to healthy control samples, whereas in sapwood these were not statistically different.