Abstract: Background and Objective: In December 2019 in Wuhan (China), SARS-CoV-2 was identified as the agent responsible for the COVID-19 epidemic. The expansion of this disease encourages greater epidemiological surveillance and molecular techniques capable of making the diagnosis regardless of its variant. The objective of the current study was to compare the concordance between two molecular diagnostic techniques, Abbott RealTime m2000 SARS-CoV-2 and Cepheid Xpert Xpress SARS-CoV-2 in the diagnosis of COVID-19. Materials and Methods: A total of 92 oral and nasopharyngeal samples were tested by PCR on Abbott RealTime SARS-CoV-2 and o Cepheid Xpert Xpress SARS-CoV-2. The data were subjected to statistical analysis to evaluate their degree of concordance. Results: The two tests had an overall agreement of 94.57% (95% CI: 87.9-97.66), a positive agreement of 100%, a negative agreement of 90% with a Kappa coefficient κ = 89.15% (95% CI: 68.84-100). About 5 samples tested negative on Abbott were positive on Cepheid with high Ct values (Ct: Cycle threshold) greater than 40. The correlation coefficient was r = 0.82, (p = 2.2×10–16) and showed good similarity in performance. Conclusion: The two techniques are comparable in terms of performance because the results showed excellent agreement. The Cepheid technique with more amplification cycles has a better detection threshold.