Genome size varies 64,000-fold across all eukaryotes, but the evolutionary forces that shape genome size are incompletely understood. Natural selection is likely acting on genome size, as inferred from correlations with various physiological and environmental factors. There is relatively little literature when it comes to studying the effects of artificial selection on genome sizes in domesticated crops. In this project, intraspecific variation was studied between wild and domesticated accessions in the genus Gossypium using flow cytometry. Whole genome resequencing data were also used to analyze repetitive elements for increased or decreased abundance. Both genome size and particular repetitive families increased in domesticated relative to wild accessions of Gossypium hirsutum, and repetitive DNA content and possibly genome size were significantly different in G. herbaceum. Instances of intraspecific variation, as demonstrated here, provide insight into the evolutionary forces acting on genome size in a brief evolutionary period.