Eukaryotic genomes vary remarkably in size even between closely related species. This variation reflects a balance between mechanisms that expand and contract genomes, and which vary in their magnitude during evolution. While much is known about mechanisms that affect genome size expansion, particularly the effects of transposable elements (TEs), less is known concerning deletional mechanisms and the rates and scales at which they operate. The goal of this thesis was to extend our understanding of genome size evolution by studying diploid Gossypium species that vary twofold in genome size as well as their polyploid derivative, and using a phylogenetic approach employing as an outgroup Gossypioides kirkii. We assessed the rates and mechanisms operating in four Gossypium genomes: the two co-resident genomes of the allopolyploid G. hirsutum and its model diploid progenitors, G. arboreum and G. raimondii. Two BAC-sized regions of the cotton genome were sequenced and analyzed with respect to the mechanisms that alter genome size, and rates of sequence change (insertions, deletions, and net) were calculated for each region and genome. These regions were similar in that they both represent gene islands with extraordinary conservation of intergenic space; however, the regions did differ in terms of amount of genome size change. Whereas the first region showed no signs of the twofold genome size difference characterizing the species, the second region mirrored this difference, as the smaller genomes were represented by half the amount of sequence as the larger genomes. Notably, while still gene dense, this region had nearly half the gene density of the previous region. Analysis of the mechanisms responsible for shaping these regions led to several conclusions. First, genome size change is attributable to many mechanisms, some of which are unknown. Second, while TEs had the greatest impact on genome size differences, other mechanisms, such as intra-strand homologous recombination, played key roles as well. Finally, genomes of diploid Gossypium species have experienced growth, whereas the polyploid has experienced contraction; however, the rates and direction of change vary between regions and over time.