Introduction: This study aimed to evaluate if single nucleotide polymorphisms (SNPs) in runt-related transcription factor 2 ( RUNX2 ) and bone morphogenetic protein 2 ( BMP2 ) are associated with different craniofacial patterns. Furthermore, we also investigated if RUNX2 and BMP2 expression in the maxilla and mandible are differently expressed according to facial phenotypes and influenced by the SNPs in their encoding genes. Orthognathic patients were included. Materials and Methods: Lateral cephalometric radiographs were used to classify facial phenotypes based on Steiner's ANB and Ricketts’ NBa-PtGn angles. Bone samples from 21 patients collected during orthognathic surgery were used for the gene expression assays. DNA from 129 patients was used for genotyping the SNPs rs59983488 and rs1200425 in RUNX2 and rs235768 and rs1005464 in BMP2 . The established alpha was 5%. Results: A statistically significant difference was observed in the relative BMP2 expression in the mandible between Class I and III participants ( P = 0.042). Homozygous GG (rs59983488) had higher RUNX2 expression ( P = 0.036) in the mandible. In maxilla, GG (rs1200425) had a higher BMP2 expression ( P = 0.038). Discussion: In conclusion, BMP2 is expressed differently in the mandible of Class I and Class III participants. Genetic polymorphisms in RUNX2 and BMP2 are associated with their relative gene expression.