OBJECTIVES: To evaluate the genomic epidemiology of SARS-CoV-2 from Venezuelan migrants living in Colombia. METHODS: SARS-CoV-2 from 30 clinical specimens collected from Venezuelan migrants were sequenced. Genomes were compared with the Wuhan-reference-genome to identify polymorphisms, reconstruct phylogenetic relationships, and perform comparative genomic analyses. Geographic, sociodemographic and clinical data were also studied across genotypes. RESULTS: We demonstrate the presence of six distinct SARS-CoV-2 lineages circulating among Venezuelan migrants, as well as the close relationship between SARS-CoV-2 genomic sequences obtained from individuals living in the Venezuelan-Colombian border regions of La Guajira (Colombia) and Zulia (Venezuela). Three clusters (C1, C2 and C3) are well-supported by phylogenomic inference, supporting the hypothesis of three potential transmission routes across the Colombian-Venezuelan border. These genomes included point mutations previously associated with increased infectivity. A mutation (L18F) in the N-terminal domain of spike protein that has been associated with compromised binding of neutralizing antibodies was found in 2/30 (6%) of the genomes. We identified a statistically significant association with symptomatology for cluster C2. CONCLUSION: The close phylogenetic relationships between SARS-CoV-2 genomes from Venezuelan migrants and from persons living at the Venezuela-Colombian border, supports the importance of human movements for the spread of COVID-19 and for emerging virus variants.