Rat molars and incisors have different root patterning mechanisms: the former form a multirooted pattern while the latter form a single-rooted analogue. But the genetic signals that control root patterning are poorly understood. In this study, to identify the special molecular signals which may lead to the molar root development, we firstly observed that at embryonic day 19 the molar and the incisor began differentially developing: the molar formed double-layered cells of the root sheath while the incisor formed a cervical loop. By using the subtractive hybridization method, we successfully constructed a subtraction cDNA library of the rat molar and incisor tissues. Differentially expressed gene clones were evaluated by dot-blot and sequencing. Sel1l, Nfic, Edar, GATA6, and some novel genes were found differentially expressed, which were strongly related the tooth root patterning. It is anticipated that further study of genes identified will provide insights into their specific roles in the tooth root patterning.