Rapid advancement in DNA and genomic technologies in the last decade has greatly facilitated application of marker-assisted selection (MAS) and exploitation of genomic selection (GS) in cotton breeding. In this chapter, I first discussed the technological foundations for successful MAS and GS discoveries. These include high-quality genome assemblies of diploid and tetraploid cotton species, SNP arrays with variable number of markers, novel populations for trait analysis, and new methods to analyze gene functions. Then I reviewed recent studies in trait QTL analysis and gene identification using genome-wide association study (GWAS) and transcriptome-wide association study (TWAS) with focus on my own research of analyzing a MAGIC population. I suggest that epistasis is a major contributor to the fiber phenotypic variance. Next, I provided a brief summary on MAS application in cotton breeding and GS research in cotton. MAS has been widely used to assist selection of traits controlled by a few major genes such as disease resistance and fiber strength and length. Although GS research is still at the early stage in cotton, it holds a great potential for quantitative trait improvement. Genomics-based breeding techniques will not only advance our knowledge in basic science but also speed up breeding process with reduced cost.