Abstract Background SARS-CoV-2 revealed important gaps in infectious disease surveillance. Molecular epidemiology can help monitoring and adapting traditional surveillance to surpass those limitations. This work aims to contrast data driven from traditional surveillance with parameters inferred from molecular epidemiology in Latin America (LATAM) Methods We obtained epidemiological data up to 4 th June, 2020. We estimated Effective Reproductive Number (Re) and epidemic curves using maximum likelihood (ML). SARS-CoV-2 genomes were obtained from GISAID up to June 4 th 2020. We aligned sequences, generated a ML phylogenetic tree, and ran a coalescent model Birth Death SIR. Phylodynamic analysis was performed for inferring Re, number of infections and date of introduction. Findings A total of 1,144,077 cases were reported up to 4 th June 2020. Countries with the largest cumulative cases were Chile, Peru and Panama. We found at least 18 different lineages circulating, with a predominance of B.1 and B.1.1. We inferred an underestimation of the daily incident cases. When contrasting observed and inferred Re, we did not find statistically significant differences except for Chile and Mexico. Temporal analysis of the introduction of SARS-CoV-2 suggested a detection lag of at least 21 days. Interpretation Our results support that epidemiological and genomic surveillance are two complementary approaches. Even with a low number of genomes proper estimations of Re could be performed. We suggest that countries, especially developing countries, should consider to add genomic surveillance to their systems for monitoring and adapting epidemiological control of SARS-CoV-2.