Though the first case of oral cancer related to HPV was reported in 1983, it was only in 2007, when WHO confirmed the role of human papilloma virus (HPV) in oropharyngeal cancer. Before this, the considered arch criminal for oropharyngeal cancer was primarily tobacco. In the last decade, there has been a sudden increase in oropharyngeal carcinoma in young individuals not being associated with tobacco and alcohol history. The reason could be delayed exploration of the association of HPV and oropharyngeal cancer. Out of about 100 types of HPV strains discovered at least 15 have an oncogenic potential. Of these, 90% of oropharyngeal cancer has been found to be caused by HPV 16 type strain. In recent years, many biomarkers have published on diagnosis, investigations and therapy of HPV associated oropharyngeal cancer. These biomarkers range from simple Messenger Ribonucleic Acid (RNA) of Early phase (E) E6 and E7 protein to Testicular Cell Adhesion Molecule 1 (TCAM1), Synaptonemal Complex Protein 2 (SYCP2) and Stromal Antigen 3 (STAG3). This review will encompass the molecular mechanisms associated with HPV and its carcinogenesis. The mechanisms included are interference in WNT and Notch signaling pathway leading to alteration in keratinocyte differentiation and activation of Phosphatidylinositol 3-Kinase (PI-3K) pathway. The other mechanism includes the patterns of methylation of HPV DNA and its impact over prognosis. The main aim of this review is to focus on recent patents on biomarkers for diagnosis and assessment of prognosis of HPV associated oropharyngeal cancer.