Cotton is a valuable ber crop which supplies raw material to more than 50 industries and is produced in more than 70 countries worldwide thus, it is worthy of its reputation as "white gold". The superiority of cotton ber over other crops is primarily dependent on its quality. However, further improvements in ber length, strength and neness are required for modern processing technology and for cotton to maintain its position in the global market. Association mapping enables identi cation of QTLs controlling ber quality-related traits which can be useful in cotton breeding. In the present study, we performed genetic diversity, linkage disequilibrium and association mapping analyses in 157 G. hirsutum multi-parent recombinant inbred lines using a total of 102 SSR markers. The population had depressed genetic variability (14%), a result of inbreeding of modern cotton genotypes. Despite this, we identi ed 13 signi cant and stable marker-trait associations for seed cotton yield, lint percentage, ber length, ber strength and ber neness (p < 0.005). We also detected QTL co-localizations with positive and negative marker additive effects. Our results indicate that selection against negative alleles may be as important as selection for positive alleles. Analysis of the effects of allelic combinations at different QTLs revealed signi cant and stable marker clusters that can be selected for or against to provide maximum quality gains in cotton ber quality.