In this study the extent of linkage disequilibrium (LD) and association mapping of fiber and agronomic characters is assessed using 11 Egyptian cotton genotypes and 116 random amplified polymorphic DNA markers (RAPDs).  The studied genotypes, using Bayesian algorithm, showed weak population structure and were assigned to three admixed clusters.  Additionally, high level of relatedness was observed conforms to full- and half-sibs relationship.  The LD showed slow decay with distance (< 50 cM).  The population structure and relatedness are considered while conducting association mapping.  Consequently, the Unified Mixed Model approach was used to account for population/family structures by inclusion of population structure (Q) and kinship (K) matrices.  With such considerations, a total of five significant associations were observed between RAPD and agronomic characters.  Among these associations single RAPD marker concurrently associated with three traits.  These findings highlight the potential of association mapping in Gossypium barbadense considering population and family structure.  Also the co-association would accelerate the marker assisted section (MAS) programs as a single marker could be utilized to breed for multiple correlated traits.