Novel coronavirus (SARS-CoV-2) pandemic has impacted the world severely causing millions of positive cases and thousands of fatality cases. Admission of a large number of infected patients in the hospitals is creating daily challenges for medical experts and researchers, such as limited numbers of isolation rooms, less amount of personal protective equipment (PPE), maintaining the hygiene in the hospitals, handling of many clinical samples for tests at the laborites, etc. This disease is mild in most people, but in pre-medical conditions and some elderly people, this virus is affecting majorly and causing fatality. Symptoms of this viral infection include pneumonia, acute respiratory diseases, and multi-organ dysfunction. Considering the situation, early diagnosis of the disease is extremely crucial to control the ongoing epidemic. In this chapter, we have summarized current molecular assays that are in use at many laboratories and hospitals for coronavirus detections. We also discussed molecular diagnosis cases of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) viruses. Many improved and new approaches of molecular tools are involved for the detection of these viruses that are listed down in the table form. We have also reviewed the current challenges/issues arising currently for the effective diagnostics and treatment of the pandemic situation. Further, we put heads together about the future directions