Mosquito-borne viral diseases, including dengue, Zika, chikungunya, and West Nile virus, pose significant public health challenges worldwide. Molecular diagnostics play a critical role in the early detection and management of these infections. This chapter explores various molecular approaches, including conventional polymerase chain reaction (PCR), real-time PCR, reverse transcription PCR (RT-PCR), loop-mediated isothermal amplification (LAMP), and next-generation sequencing (NGS). A comprehensive review of commonly used PCR primers for detecting specific viral genomes is provided, highlighting their sensitivity and specificity. Despite advancements in molecular diagnostics, several challenges remain, particularly in epidemiological surveillance and field applications. Issues such as sample degradation, cross-contamination, logistical constraints, and limited access to high-throughput technologies hinder effective disease monitoring in endemic regions. Additionally, viral genetic variability and co-infections complicate accurate detection. Emerging concepts, including portable PCR platforms, CRISPR-based diagnostics, and metagenomic approaches, offer promising solutions for rapid and reliable field detection. The integration of molecular diagnostics with surveillance programs is essential for real-time outbreak response and public health interventions. This chapter underscores the need for continuous refinement of molecular tools to improve diagnostic accuracy and field applicability in combating mosquito-borne viral diseases.