Objectives: This review aims to find the general profile of salivary nucleic acids; to understand the current detection method of salivary viral DNA and RNA, and to understand the prospect of metagenomic analysis for salivary viral infection. Method: This review was started with searching processes with the help of PubMed, during August 2020. After screening the articles, 64 articles were obtained and used as referents. Results: Salivary nucleic acids contain viral DNA and RNA that can be used as biomarkers for virus infection. Even the salivary amount of DNA/RNA is very tiny, it is definite and associated with the viral infection. Viral DNA and viral RNA in saliva are categorized into two groups, the gland salivary viral DNA/RNA and systemic viral DNA/RNA. Most of the current PCR-based methods are single genomic analysis that can not detect multi strains community of pathogenic viruses. Multiple genomic analysis is needed to be implemented for multi strains of viral infection. Conclusions: The presence of viral nucleic acids in the saliva is associated closely with the glands salivary and the systemic viral infections. Therefore, they are useful biomarkers for the diagnosis of viral diseases. In the future, the metagenomic analysis can be applied for the multi strains of viral analysis.