Cotton not only provides the world's best natural spinnable fibre but also its seed is a rich source oil and protein, which is best for food and livestock feed. A biotic and biotic stresses always a serious threat to cotton production world widely. There is a demand of such cultivars which could oppose these stresses with wide genetic variability. Molecular breeding along with marker technology opened new ways in crop improvement. Genome mapping which is the identification of genomic regions linked with different traits; using construction of linkage map and quantitative trait loci (QTL) analysis can be used to identify resistant sources with the use of marker assistant selection (MAS). Improvements in control of many biotic diseases like verticillium (V) and Fusarium Wilt (FW), Reniform and Root-knot Nematodes had been made using molecular breeding. Cotton leaf curl disease (CLCuD) is the most distressing diseases of cotton in Pakistan, north-western areas of India and some parts of Africa which could be improved using these biotechnological tools. In many agricultural crops viral diseases like tomato yellow leaf curl virus (TYLCV), tomato mosaic virus (ToMV), tomato spotted wilt virus (TSWV), rice black-streaked virus (RBSV), Maize Streak Virus (MSV), Maize dwarf mosaic virus (MDMV), Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV), Maize chlorotic dwarf virus (MCDV), Maize mosaic virus (MMV), Maize fine streak virus (MFSV), Rice Stripe Virus (RSV), Rice yellow mottle virus (RYMV), rice black-streaked dwarf virus (RBSDV) and Barley Yellow Dwarf Virus (BYDV) had been studied using molecular markers.This Review study provides explanation of molecular markers involved in crop improvement especially for disease resistance in cotton and other field crop which could carry out to find out CLCuD resistant sources in upland cotton.