The pandemic due to the SARS-CoV-2 virus, the etiological agent of Coronavirus Disease 2019 (COVID-19), has caused immense global disruption With the rapid accumulation of SARS-CoV-2 genome sequences, however, thousands of genomic variants of SARS-CoV-2 are now publicly available To improve the tracing of the viral genomes ’ evolution during the development of the pandemic, we analyzed single nucleotide variants (SNVs) in 121,618 high-quality SARS-CoV-2 genomes We divided these viral genomes into two major lineages (L and S) based on variants at sites 8782 and 28144, and further divided the L lineage into two major sublineages (L1 and L2) using SNVs at sites 3037 , 14408, and 23403 Subsequently, we categorized them into 130 sublineages (37 in S , 35 in L1, and 58 in L2) based on marker SNVs at 201 additional genomic sites This lineage/sublineage designation system has a hierarchical structure and reflects the relatedness among the subclades of the major lineages We also provide a companion website (www covid19evolution net) that allows users to visualize sublineage information and upload their own SARS-CoV-2 genomes for sublineage classification Finally, we discussed the possible roles of compensatory mutations and natural selection during SARS-CoV-2 ’ s evolution These efforts will improve our understanding of the temporal and spatial dynamics of SARS-CoV-2 ’ s genome evolution