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Human papillomavirus (HPV)–associated oropharyngeal squamous cell carcinomas (OPSCCs), predominantly driven by HPV16, constitute a clinically and biologically distinct entity from HPV-negative OPSCCs. Although these tumors generally have a more favorable prognosis and better response to standard treatments, approximately 10–25 % of patients experience recurrence following curative therapy. Currently, no validated biomarkers are available to identify patients at risk of relapse. This review covers: (i) the molecular bases distinguishing HPV-positive from HPV-negative OPSCCs; (ii) the heterogeneity of HPV-positive OPSCCs, with a particular focus on viral heterogeneity; and (iii) emerging molecular virological tools applicable in the context of HPV-positive OPSCCs. These viro-centric approaches include the detection and quantification of circulating tumor HPV DNA using digital polymerase chain reaction (dPCR), as well as whole viral genome sequencing, which is instrumental for investigating viral heterogeneity within these tumors. Taken together, these tools offer promising avenues for improving prognostic stratification and personalized monitoring of patients with HPV-positive OPSCCs. They are expected to facilitate the identification of biomarkers suitable for routine clinical use, thereby supporting therapeutic de-escalation strategies and reduced-intensity post-treatment surveillance.