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There are very few studies in search of an alternate and convenient diagnostic tool which can substitute nasopharyngeal swab (NPS) specimen for detection of SARS‐CoV‐2. In the study we analyzed, the comparison and agreement between the feasibility of using the saliva in comparison to NPS for diagnosis of SARS‐CoV‐2. A total number of 74 patients were enrolled for this study. We analyzed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. We carried out real‐time quantitative polymerase chain reaction, gene sequencing for the detection and determination SARS‐CoV‐2 specific genes. Phylogenetic tree was constructed to establish the isolation of viral RNA from saliva. We used the Bland–Altman model to identify the agreement between two specimens. This study showed a lower cycle threshold (CT) mean value for the detection of SARS‐CoV‐2 ORF1 gene (mean, 27.07; 95% confidence interval [CI], 25.62 to 28.52) in saliva methods than that of NPS (mean 28.24; 95% CI, 26.62 to 29.85) specimen although the difference is statistically nonsignificant (p >.05). Bland–Altman analysis produced relatively smaller bias and high agreement between these two clinical specimens. Phylogenetic analysis with the RdRp and S gene confirmed the presence of SARS‐CoV‐2 in the saliva samples. Saliva represented a promising tool in COVID‐19 diagnosis and the collection method would reduce the exposure risk of frontline health workers which is one of the major concerns in primary healthcare settings. Highlights: We analysed and compared the NPS and saliva specimen collected from 74 individual within 48 h after the symptom onset.This study showed a lower cycle threshold (CT) mean value for the detection of SARS‐CoV‐2 ORF1 gene in saliva methods than that of NPS specimen.Phylogenetic analysis with the RdRp and S gene confirmed the presence of SARS‐CoV‐2 in the saliva samples.Saliva represented a promising tool in COVID‐19 diagnosis. [ABSTRACT FROM AUTHOR]