Masseter muscle is one of the masticatory muscles functioning in mandibular elevation. Its anatomical structure is closely related to the underlying skeletal structure. Thus, changes happened in the muscle structure will affect the growth of the jawbones. Numerical studies have been conducted to demonstrate and correlate the changes in masseter muscle to the skeletal malocclusion. Changes in fiber type properties, genetic, and epigenetic expression of masseter muscle resulting in a significant correlation to specific malocclusion. Single nucleotide polymorphisms (SNPs) is a common type of genetic variation that induced changes in genetic expression of masseter muscle. Nonsense mutation of R577X in ACTN3 gene is one evidence of genetic expression influence on developing skeletal deep-bite malocclusion. While epigenetic mechanism of acetylation and deacetylation promote by acetyltransferase (KAT) and deacetylase (HDAC) will give influence on the transcription of MHC gene.