Human papillomavirus (HPV), a major etiological factor of cervical cancer and other anogenital malignancies, having more than 200 genotypes divided into five genera alpha(α), beta(β), gamma(γ), mupa, and nupa, out of which 40 are associated with cancer and other malignancies. Traditional methods of diagnosis such as cytology and histopathology show compromised sensitivity and specificity, leading to a growing reliance on molecular techniques. Molecular diagnosis of HPV plays a crucial role in early detection, genotyping, and disease management. Recent advancements Polymerase-chain-reaction (PCR)-based and CRISPR-based diagnostics assays offer high sensitivity and specificity for HPV detection and genotyping with improved accuracy, rapid results, and cost-effective screening. Additionally, isothermal amplification methods such as loop-mediated-isothermal-amplification (LAMP) have emerged as promising point-of-care diagnostic tools. The integration of biosensors, microfluidics, and artificial intelligence in HPV diagnostics is further enhancing precision and accessibility. Despite these advancements, challenges such as cost, accessibility in low-resource settings, and the need for standardized protocols still exist. In this chapter, we highlight the current trends and recent approaches in molecular diagnosis of HPV, and their potential utilization in clinical practices. The development of rapid, accurate, and affordable molecular diagnostic tools will improve HPV screening programs and reducing the global burden of HPV-associated diseases.