Diploid A genome cottons are grown for their natural fiber in drought prone areas of Asia. Although they possess inferior fiber qualities to cultivated Upland and Pima cotton, their value lies in their inherent resistance to pests and diseases. Molecular linkage maps provide essential tools for plant genetic research, facilitating quantitative trait locus (QTL) mapping, marker-assisted selection and map based cloning. In the present study, we used SSR, AFLP, and TRAP markers to construct a linkage map using 94 F2 diploid individuals derived from a cross between G. arboreum x G. herbaceum. A total of 606 polymorphic markers were used to construct 37 linkage groups covering a total of 1109cM with an average distance of 7.92cM between two loci. Discriminant analysis identified three markers each associated for petal color and seed fuzziness, and four markers for petal spot. For quantitative traits, a total of 19 QTL were identified for five fiber traits using composite interval mapping. The identified QTL’s such as qFL4-1, qFS4-2, qELO1-1 and qSI2-1 were found to be significantly linked to fiber length, strength, elongation and seed index, respectively. This work could lead to more such attempts in deploying markers onto the A genome, thus guiding QTL mapping in tetraploid cottons.