The herbicide resistance to dicamba (HRd) biotype of kochia is resistant to several auxinic herbicides and is impaired in shoot gravitropism and other auxin-mediated responses. To better characterize the biotype and investigate its mechanism of resistance, we used messenger RNA (mRNA) differential display to compare patterns of dicamba-induced gene expression in HRd and susceptible (S1) plants. More than 60,000 complementary DNA fragments were generated and examined, 106 of which were isolated and used as probes on Northern blots to confirm gene expression levels. Steady-state levels of > 90% of mRNAs did not change after dicamba application. However, several mRNAs were detected whose levels were decreased, increased, or differentially regulated between the biotypes within minutes of dicamba treatment. The abundance of three mRNAs decreased after treatment, two of which had significant sequence similarity to choline monooxygenase and 5,10-methylenetetrahydrofolate reductase, respectively. Conversely, increased expression levels were observed for a putative chloride channel protein, 1-aminocyclopropane-1-carboxylate synthase, and an unknown gene. Genes differentially expressed between HRd and S1 plants included those similar to a putative translation initiation factor, xyloglucan endotransglycosylase, and a hypothetical protein cloned from several organisms. The results demonstrate that mRNA differential display is a useful technique for discovering genes that are rapidly regulated as part of a physiological response, and that this approach may provide insight into the mechanism of auxinic herbicide resistance in kochia.