Cotton is one of the most important crops in the world as the fiber crop; besides, it is also an important oil crop. Like other crops, most of the agronomic traits, such as yield, fiber quality, and biotic and abiotic stresses, are quantitative traits that are controlled by many quantitative trait loci (QTLs). To mapping QTLs underlying these traits, linkage analysis and association mapping are two traditional and popular methods. From 1998 to 2021, thousands of QTLs related to hundreds of traits in cotton have been mapped from interspecific (crosses between other tetraploid species and Upland cotton) and interspecific (within Upland cotton) populations (CottonQTLdb, http://www2.cottonqtldb.org:8081/index ). However, cotton researchers found that most of these QTLs are parent-population specific and environmental unstable, which is very hard to apply them in marker-assisted selection to improve efficiency in cotton breeding. Among the two mapping methods, linkage analysis only captures major variations between two parents that are not widespread in the popular breeding germplasm; and the mapping resolution is lower in linkage analysis resulted from limited recombination during segregation population development. Cotton researchers are trying association mapping to uncover the genetic basis of complex traits in cotton. In this chapter, I summarize main achievements in cotton GWAS that were published in popular international journals.