Phenological traits, e.g. dormancy, are mechanisms by which perennial tree species have adapted to stressful conditions that are unfavorable for growth. While there are many mechanisms by which trees adapt and respond to stress, the phenylpropanoid pathway in particular is known to be associated with tree stress response. In this study, Prunus persica (peach) and P. armeniaca (apricot) were used as models to explore the relationship between phenylpropanoids and adaptive trait variation. Concentrations of eight phenylpropanoid intermediates were measured throughout dormancy in floral buds of trees that differed genotypically and phenotypically in chill requirement (peach) and bloom date (apricot). There was a significant interaction effect of time and genotype on the concentration of each of the compounds (mixed ANOVA, P < 0.05). Moreover, concentrations of the flavonoid aglycones, apigenin, kaempferol, and quercetin, dropped precipitously in high chill peach and late flowering apricot, around the endodormancy-ecodormancy transition and at the time when buds began to show signs of blooming (e.g. presence of sepals and petals). These results suggest a potential role of phenylpropanoid intermediates in mediating the resumption of growth and development following winter dormancy. A better understanding of tree responses to stress, will be critical for tree improvement programs aimed at identifying and breeding trees more suitable for rapidly changing environments.