The nuclear gene SAMT—salicylic acid methyltransferase—is a novel phylogenetic marker that was isolated using RT-PCR in order to estimate intergeneric relationships within the Solanaceae. SAMT catalyzes the formation of the volatile compound methyl salicylate, which is an important secondary metabolite for both pathogen defense and floral fragrance in this family. Relationships inferred with SAMT cDNA sequences are mostly congruent with previous cpDNA estimates, which not only increases our confidence in Solanaceae phylogeny, but indicates that paralogy and lineage sorting appear not to be severe for this nuclear gene at this phylogenetic level. Relationships observed with SAMT include Schizanthus as sister to the rest of the family. The second branch was Schwenckioideae Cestroideae. The final two lineages were Petunioideae sister to the x=12 clade, which includes Nicotianoideae Solanoideae. Although mostly congruent, one important phylogenetic difference between previous cpDNA and nuclear SAMT phylogenetic estimates is noted. Nicandra and Exodeconus are not supported as sister taxa; rather, Exodeconus is near the base of the Solanoideae while Nicandra appears to belong to a lineage that includes Physalis, Capsicum, Solanum, and Datura. The results obtained in this study indicate that expanded sampling of taxa for SAMT and the study of additional nuclear gene sequences in conjunction with cpDNA will be valuable towards improving our understanding of Solanaceae phylogeny.