Over 90 percent of the world’s cotton is upland cotton or Gossypium hirsutum L. (Brubaker et al., 1999); this chapter will concentrate on this one species. A passing reference will be given to Gossypium barbadense L., since it is the second most important cotton species; this species includes Sea Island, Egyptian, and Pima cottons, along with extra-long staple cottons of other countries such as India, Peru, Sudan, and the former Soviet Union. Both of these species are allotetraploids with 2n = 52 chromosomes, and both have “A” and “D” subgenomes. Allotetraploids are native only to the New World, although G. hirsutum is grown extensively throughout the world. The A subgenome is characteristic of the Old World diploid cottons (2n = 26), G. arboreum L. and G. herbaceum L. The D subgenome is characteristic of the New World diploid cottons, of which there are at least a dozen wild species. The A subgenome consists of relatively large chromosomes, while the D subgenome has relatively small chromosomes. It is theorized that the tetraploids resulted from natural hybridization of an Old World and a New World diploid.