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Background: Attempts should be made to identify the molecule-based biomarkers, which give indication about the progression of precancer and malignancy of the oral area. Aim: To evaluate the reliability of methylation of genes of saliva like P16, MGMT, and DAP-K as biomarkers for diagnosis of oral squamous cell carcinoma. Methods and Materials: This study included 30 cases of histopathologically proven cases of oral squamous cell carcinoma. This study was conducted to detect demethylation of genes P16, MGMT, and DAP-K in saliva in these patients. Approximately, 1 mL of saliva was collected from each individual. Bisulfite sequencing PCR (BSP) was done with bisulfite conversion-specific primers produced by MethPrimer. The BSP compounds will be quantified on a one percent agarose gel. A fraction of the products obtained in BSP were then analyzed with the help of qMSP. Results: The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of methylation of genes P16, MGMT, and DAP-K as biomarkers of oral carcinoma were statistically significant. In our research, there were some very important useful findings regarding the possibility of the use of deoxyribonucleic acid methylation as a potential biomarker for the progression of premalignancy and malignancy of oral cavity, which need to be further followed up. Conclusion: Salivary biomarkers like P16, MGMT, and DAP-K can be used in the diagnosis of oral squamous cell carcinoma.