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Cotton (Gossypium spp.) is a major cash crop of India and is the second-largest cotton producer in the world after China. Gossypium hirsutum and Gossypium barbadense are two tetraploid species that are majorly cultivated besides two diploid species (desi cotton). In cotton, fiber quality, drought tolerance, boll weight, boll number, and yield are essential quantitative traits with many components that are controlled by several genes present at different loci. Identifying such genes from different genomic resources of cotton using various molecular markers is necessary to accelerate the Quantitative Trait Loci (QTL) analysis. In the public domain of cotton, there is a vast number of molecular markers. However, not all are very useful for trait mapping, as most markers are away from the QTL region. Thereby, cotton improvement programs pay more attention to tightly linked markers with high predictive trait values. The present review provides an overview and updates on the comparative studies and the application of various molecular markers, i.e., RFLP, AFLP, RAPD, SSR, EST-SSR, and SNP in the cotton-breeding program. Insights gained from the study may help in successful cotton breeding and improvement.