The genetics of high quality lint is complex which hinders the breeding progress towards for achieving the high lint yield and quality. Integration of DNA markers for selecting the desirable cotton plants producing the high quality fiber can accrelelate the breeding progress. In this regard, 289 diverse cotton genotypes developed in different cotton growing countries were subjected to charcaterise for ginning outturn (GOT) percentage and fiber qaulity triats. Genotyping-by-sequencing (GBS) assay identified 4730 single nucleotide polymorphsims (SNPs) in these genotypes. In total 332 marker-trait assocations were found. A total of 11 significant SNPs were found for GOT percentage. Out of the 41 SNPs associated with staple length, 11 were found the most signficant, of these seven were mapped to Chr-19. Out of these, the most signficant SNPs ‘A8810’ and ‘A9078’ were identified by both the models using GLM and MLM. Out of the 32 QTLs identified, 11 QTLs were novel. Out of these, four QTLs for fiber length were showing larger impact on the trait, i.e. qFL (P=1.1E-06; R2= 0.17875), qFL (P=3.7E-06; R2= 0.21967), qFL (P=0.000013; R2=0.19023) and qFL (P = 0.00001; R2=0.16858). Similarly, for fiber maturity, our of the three novel QTLs, one expressed larger impact on fiber maturity trait (P=0.00003; R2=0.1695). Therefore, we concluded that SNPs can be used as canidate markers for fiber traits which will ultimately assist in marker-aided selection.