The traits related to early maturity in upland cotton are quantitative traits usually affected by multiple genes and environments, it is difficult to dissect their genetic basis. However, both linkage mapping and association analysis provide new tools toward interpreting the gene sources of complex traits. In this study, two F 2 mapping populations were constructed by using upland genetic standard line TM-1 as male to cross with female parents Xinluzao 8 and Xinluzao 10, respectively. Thirty-seven QTL for traits related to early maturity were identified by the composite interval mapping (CIM) method of Win QTLCart 2.5 in the F 2 -F 2:3 of the two mapping populations . Positive alleles at these loci were mostly from early maturity ancestor 611-B and King cotton, respectively. In addition, most of the traits were controlled by different genes in the two sets of gene pools, showing primarily additive effects. Furthermore, in a natural population consisting of 43 different Upland cotton cultivars, 54 genetic loci significantly associated with early maturity related traits were detected through genome-wide association analysis, showing great comparability with the linkage mapping results. Our study provided insights into the genetic bases of early maturity and laid a foundation for early maturity gene pyramiding and marker-assisted selection of upland cotton.