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The genus Gossypium has 45-50 species, of which only four (two allotetraploids and two diploids) enjoy the status of cultivated cotton. Among the four cultivated ones, Gossypium arboreum holds a special place because of the inherent ability to withstand drought, salinity and remarkable resistance to sucking pests and leaf curl virus. However, the species suffer with poor fiber quality traits, low yield and has certain undesirable plant and boll features. Improvement of fiber quality traits of G. arboreum, without disturbing its unique characteristics, has been a long sought after dream of scientists world over. For conservation, evaluation and documentation of existing accessions, gene banks of diploid cultivated cotton has been established by different countries, of which India holds the highest number of G. arboreum collections. Traditional breeding efforts made to improve fiber quality of G. arboreum have met with limited success due to paucity of polymorphic phenotypic markers and polygenic nature of the desired traits. Genetic engineering approach is highly genotype dependent and much success has not been achieved by this way also. Molecular breeding approach, based on the strength of breeding with high polymorphic nature of molecular markers, has yielded significant results in the improvement of G. arboreum. A number of molecular markers have been developed and used in various cotton improvement programs but dominantly these efforts have been made for the allotetraploid species G. hirsutum. Some efforts have been made for generating fingerprint database of G. arboreum germplasm, though much more efforts are needed in this direction. Linkage maps of G. arboreum have been generated using different markers systems which has enabled the mapping of gene/QTLs of desired traits on the chromosome of G. arboreum. More research inputs need to be devoted to produce consensus and saturated genomic maps, if the aim of 'breeding by design', by retaining suitable features and improving the undesirable ones, is to be realized for G. arboreum.