Oral squamous cell carcinoma (OSCC) is amongst the most prevalent form of cancer worldwide with its predominance in the Indian subcontinent due to its etiological behavioral pattern of tobacco consumption. Late diagnosis, low therapeutic response and aggressive metastasis are the foremost confounders accountable for the poor 5 year survival rate of OSCC. These failures are attributed to the existence of “Cancer Stem cell (CSC)” subpopulation within the tumour environment. Quiescence, apoptotic evasion, resistance to DNA damage, abnormal expression of drug transporter pumps and in vivo tumorigenesis are the defining hallmarks of CSC phenotype. These CSCs have been distinguished from the tumor mass by determining the expression patterns of cell surface proteins, specific stemness markers and quantifying the cellular activities such as drug efflux & aldehyde dehydrogenase activity. Hence, it is necessary to understand the underlying mechanisms that regulate the CSC features in tumor development, metastasis and response to chemotherapy. Increasing evidence suggests that majority of malignant cells eventually undergoing Epithelial-Mesenchymal transition (EMT) share many biological characteristics with CSCs. Thus, this review encompasses the functional relevance of CSC and EMT markers in OSCC population with a hope to elucidate the fundamental mechanisms underlying cancer progression and to highlight the most relevant epigenetic mechanisms that contribute to the regulation of CSC features. We further aimed to explore the causal effects of nicotine, a major tobacco carcinogen, on epigenetic mechanisms regulating the OSCC CSCs and EMT markers which unravels the undisputable contribution of tobacco in oral carcinogenesis.