Molecular diagnosing of COVID-19 primarily depends on the detection of RNA of the SARS-CoV-2 virus, the contributory infective agent of the pandemic. Reverse transcription enzyme chain reaction (RT-PCR) permits sensitive detection of specific sequences of genes that cypher the RNA dependent RNA enzyme (RdRP), nucleocapsid (N), envelope (E), and spike (S) proteins of the virus. Though RT-PCR tests are wide used and plenty of different assays are developed, the present testing capability and handiness cannot meet the unprecedented international demands for fast, reliable, and wide accessible molecular diagnosing. Challenges stay throughout the complete analytical method, from the gathering and treatment of specimens to the amplification and detection of infective agent RNA and also the validation of clinical sensitivity and specificity. We have a tendency to highlight the most problems encompassing molecular diagnosing of COVID-19, as well as false negatives from the detection of infective agent RNA. We have a tendency to discuss vital analysis like enhancements in RT-PCR, development of different macromolecule amplification techniques, incorporating CRISPR technology for point-of-care (POC) applications, validation of POC tests, and sequencing of infective agent RNA and its mutations. Improved assays are required for environmental based work or waste material-based epidemiology which gauges infection on the community level through analyses of infective agent elements within the community wastewater.