For gene-enzyme systems in forest trees it is unclear how much structural genetic diversity as compared to diversity of the genetic background contributes to phenotypic variability. The gene-enzyme-system of PEPC-A, phosphoenolpyruvate-carboxylase (PEPCase, EC 4.1.1.3 I), of Norway spruce (Picea abies (L.) Karst.) was chosen as an example to investigate the relative importance of the following sources of phenotypic variation in enzyme activity: (1) Variation at the structural PEPC-A-locus with three genotypes, (2) Variation in the genetic background, (3) Variation in growth temperature. The amount, specific activity and catalytic efficiency of PEPCase in crude needle extracts were assessed as quantitative traits. According to our ANOVA results, variation in the genetic background, i.e. epistasis in the general sense, is the most important source of variation compared to variation at the levels of both PEPC-A-genotype or growth temperature. Moreover, evaluation of the kinship partition of the genetic background revealed the individual level as most important. We compare to results of similar investigations for other species with different life histories and point to consequences for forest tree conservation genetics.