We used diploid cotton accessions coming from diploid cottons main growing zones to evaluate the range of diversity represented within accessions and to address the questions of two A-genomes species distinctions. The G. herbaceum accessions were mainly collected from South Africa, Former Soviet Union, and China, while G. arboreum accessions were mostly collected from India, Pakistan, and China. If you use these data, please cite the paper: Huang G. et al. Genome sequence of Gossypium herbaceum, and genome update of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics, 2020.