Cotton germplasm needs to be enhanced in order to meet the needs of modern textile industry in USA and international competition. An exotic germplam population derived from multiple crosses among tetraploid species was used to identify association between ssr markers and fiber traits. Two hundred and sixty inbred lines were grown at two locations with two replicates each in 2005. These lines were evaluated for their agronomic performance and fiber properties. Tremendous genotypic variance was identified among the inbred lines for these traits. Variance component of genotype for all yield components and fiber properties analyzed were at least two fold greater than genotype x location. DNA was extracted from these lines and screened for polymorphic ssr primers. Eighty-eight ssr loci were screened among the lines. Two hundred and ninety-six fragments are identified polymorphic. Substructures of this population were analyzed using STRUCTURE software. Most of the lines grouped into three clusters with high probability. Genetic differentiation among the substructures was analyzed based on Fst values. Association was analyzed with the information on population substructures. Some major QTLs were identified associated with yield components and fiber properties. Some markers associated with yield components showed the same relationships among yield components. These markers can be used to dissect the complicated interrelationships among yield components.