The root-knot nematode (Meloidogyne incognita) is a serious pest of cotton. Traditional screening approaches applicable to the development of resistant varieties are time consuming, laborious and prone to environmental variability.  Recent research has identified molecular markers associated with the two genes governing resistance and offers the potential to increase screening efficiency. The present investigation focuses on the application of microsatellite markers to identify resistant segregating progeny in an applied Upland cotton (Gossypium hirsutum L.) improvement program.