The objective of this study was to investigate the effects of origin, genotype, and their interaction on multielement fingerprints in wheat kernels to provide theoretical basis for geographical traceability. Ten varieties were grown in three different regions of China during the 2010-2011 growing seasons. The concentrations of 10 elements (Na, Mg, Ca, V, Mn, Fe, Cu, Zn, Mo, and Ba) were determined in 90 wheat kernel samples and 30 provenance soil samples. Multiway analysis of variance results demonstrated that both origin and genotype had significant influences on the content of each element, and their interaction had significant influences on the contents of Mn, Fe, Cu, Zn, Mo, and Ba. The elements Na, Ca, Fe, Zn, and Mo were associated with origin, and Mg, Mn, Cu, and Ba were related to genotype. Na, Ca, Fe, Zn, and Mo were proved to be good indicators to discriminate wheat geographical origin.