The dental anomaly fused teeth is defined as the union of two or more teeth. Its aetiology is unclear; to date no studies have investigated its genetic background. Therefore, this study, on the basis of a hypothesised genetic component, investigated the genetic background of patients with fused teeth using whole exome sequencing. Fifteen individuals from six families, including members with and without fused teeth, provided saliva samples that were analysed using whole exome sequencing. Patients with other congenital diseases were excluded from this study. Rare variants were extracted from the sequencing data and filtered by family grouping to identify candidate variants. As a result, ERCC6, OBSCN, SLC27A3, and KIF25 were identified as candidate variants. Our sequencing analysis identified four candidate gene variants associated with fused teeth, which now require further investigation. A genetic basis for the anomaly appears likely. This may assist in understanding the aetiology of fused teeth, which in turn supports better oral care and treatment, as well as future regenerative medicine and gene therapy.