SSRs are new marker types recently added to the existing trispecific linkage map of Gossypium. At present this map comprises 332 AFLP, 91 RAPD, 12 SSR and 3 morphological markers. Of the 12 SSRs, 7 markers are specific to 5 chromosomes of the cotton genome (chromosomes 2-S, 5-L, 6-L, 9-L and 10-L), and 4 SSRs were found linked with existing molecular markers on 3 different linkage groups. Initially the collection of polymorphic markers comprised 43 linkage groups and a set of markers that were unlinked with any of the anchored linkage groups. When grouped among themselves, these markers formed 8 more groups and the number of linkage groups increased from 43 to 51 and covered a total distance of 6663 cM. We used only the anchored 43 linkage groups for QTL analyses of seven agronomic traits scored from the same trispecific F₂ population. A total of 67 QTLs were detected for these agronomic traits. They consisted of 10 QTLs for leaf main lobe length, 9 for leaf main lobe width, 12 for length of leaf second lobe, 14 for sinus depth, 11 for bract teeth number, 6 for internode length, and 5 for petal length. All QTL analyses were performed by the MapMaker program using a LOD threshold of 2.0 or above. Number of QTLs may increase with the addition of more markers.