Plant secondary metabolism affects ecosystem diversity and the yield and quality of feedstocks for biomass and biofuel, through an elaborate network of pathways that share common precursors. Until recently, functional dissection of these networks has depended largely on molecular information stored in the genome of Arabidopsis, an annual herb. Now that the Populus genome sequence is available, the potential for understanding and exploiting secondary metabolism in tree species comes closer to realization. In the present overview, genomic information pointing to greatly expanded gene complexity and function of the phenylpropanoid pathway in Populus is summarized. Phenylpropanoid-derived flavonoid and salicylate phenolics occur in numerous functionally distinct forms, and can account for 50% of leaf biomass in Populus and other fast-growing tree taxa. Their potential effects on tree growth, and their documented impacts on ecosystem diversity and productivity justify molecular dissection of secondary metabolism in Populus. Biosynthesis of salicylate phenolics remains poorly understood. By contrast, in silico promoter analysis of flavonoid genes, and in situ flavonoid localization in Populus reported here, augment published gene expression data, and illustrate that intra and intercellular regulatory components dramatically affect secondary carbon partitioning in this woody perennial.