When breeders cross two cotton varieties together there are millions of potential new combinations of genes that are generated in the progeny from the two parent plants. The breeders must then select from amongst these those few combinations that give an improvement in varietal performance (eg. yield, fibre quality, disease tolerance). In many cases this requires the assessment of many thousands of lines in small evaluation plots over multiple seasons to come up with those elite performers that are then evaluated in large scale variety trials and a selection of which will become a new variety. Any new tool that will help the breeder follow useful agronomic characteristics through a breeding population and reduce the number of lines that need to be evaluated in the field will increase the efficiency and speed with which new varieties can be developed. DNA or molecular markers are one such tool that is now being used widely for fundamental genetic studies in plant biology, but increasingly in commercial and institutional breeding programs for crops, such as maize and wheat (where incremental advances in yield have become difficult to achieve by conventional strategies). DNA markers have yet to have any major impact on cotton breeding.