The aim of this study was to screen for differential expression of signaling pathways in odontogenic differentiation of ectomesenchymal cells isolated from the first branchial arch of embryonic day 10 (E10) mice by real time RT-PCR microarray. Observations of cellular morphology, immunocytochemistry, and RT-PCR were used to identify the cell source. A real time RT-PCR microarray was then used to detect the differential expression of signaling pathways in cells dissected from animals at two different developmental stages. These assays identified 25 up-regulated genes and 16 down-regulated genes involved in odontogenic differentiation of the ectomesenchymal cells of the first branchial arch. They represented the main members of Wnt, Hedgehog, TGF-β, NF-κB, and LDL signaling pathways. This study determined that these signaling pathways are important for odontogenic differentiation of ectomesenchymal cells of the first branchial arch.