Epigenetics is the study of inheritable changes in gene expression without changes in the underlying deoxyribonucleic acid (DNA) sequence. The main mechanisms of epigenetic regulation include DNA methylation, modifications in histones, and micro-ribonucleic acids (miRNA). Recent research evidence has shown that environmental and lifestyle factors dynamically interact with the genome, influencing epigenetic changes, from development to the later stages of life. This happens across a spectrum, from physiological to pathological conditions, such as genetic defects, developmental disorders, infectious or inflammatory processes, cancers, mental disorders, and substance abuse. Epigenetic studies have been conducted in various medical disciplines (e.g., oncology, internal medicine or psychiatry), adding valuable insight to standard medical approaches. However, in stomatology, epigenetic research is still in its infancy; thus, this review is aimed at presenting the role of epigenetic mechanisms in diseases of the oral cavity, including periodontal diseases, caries, developmental anomalies, and oral carcinoma. In addition, this paper reveals new insights into epigenetic biomarkers that can be helpful in the detection, early diagnosis, prognosis, and treatment of different oral diseases. Moreover, this review is focused on the possible clinical implications (diagnostic and therapeutic) of epigenetics, in the form of some noninvasive methods that can possibly be used in the future for the screening, work-up, outcome prediction and novel treatments of some dental diseases. Finally, this paper highlights that an epigenetic approach can be useful for designing novel interventions that will improve the management of oral malignancies or developmental abnormalities.