Improving fiber quality of naturally colored cotton has become more important in recent years due to changes in the spinning technology and consumer demand. The identification of quantitative trait loci (QTL) closely linked to the fiber quality traits can allow marker assisted selection (MAS) which leads us to future’s improved cotton cultivars. In this study, we performed genetic mapping on F2 population of G. hirsutum (Yesil × Nazilli 84) intraspecific cross, and identified QTL for fiber color parameters (L, a, b, ∆L, ∆a, ∆b, ∆E) and fiber quality traits (fiber length, uniformity and elongation). The resulting genetic linkage map comprised of 123 amplified fragment length polymorphism (AFLP) markers and 27 linkage groups (LGs), covering 2068.5cM with an average distance of 16.8cM between two markers. Using single marker analysis a total of 43 QTL for fiber color parameters and fiber quality traits were identified, including four for fiber length, two for fiber uniformity, two for fiber elongation, five for L, four for a, four for b, eight for ∆L, four for ∆a, four for ∆b and six for ∆E. The identified QTL for fiber color parameters and fiber quality traits explained between 7.8% and 14.6% and between 5.9% and 14.7% of the phenotypic variation, respectively. Additionally, recombinant individuals having green fiber color together with long fiber length, high fiber uniformity and elongation were obtained in the segregating population. These individuals can be used to develop new cotton varieties in the future.