Sequencing of SARS-CoV-2 provides essential information on viral evolution, transmission, and epidemiology. In this study, we performed whole-genome sequencing of SARS-CoV-2 using nanopore and Illumina short-read sequencing to describe the circulation of the virus lineage in Armenia. This dataset contains Nextstrain configuration files, the auspice JSON file, BEAST output logs, and trees files, and resulting log and tree files as well as R scripts and data files used in phylogenetic and functional analyses.