The whole-genome sequences of 15 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains from nasopharyngeal swab samples collected in the Republic of Moldova in June 2020 to September 2021 were determined. Little variability was observed in the early stages, when mostly clade 19A was circulating, followed by clade 20B. Later, multiple introductions of SARS-CoV-2 lineages B.1.1., B.1.1.7, and B.1.1.525 were detected. The B.1.1.7 lineage became predominant between December 2020 and June 2021, followed by the Delta variant.