This study aimed to identify the relationship between agronomical traits, yield components and molecular markers among 37 genotypes of Egyptian cotton . Two experiments were done in this work, the first one was concerned to studying  morphological traits ,as well as, yield and its component. The second experiment was carried out using different molecular markers to characterize the relationship between polymorphism of ten agronomic traits using different ways of molecular markers based-PCR i.e., RAPD, ISSR and SSR. Many primers gave polymorphic bands which could be considered as a positive or negative markers for agronomical traits and yield components traits based upon the presence or absence of unique band (s) in a specific genotype. The results indicated that the SSR technique was more effective in detecting high level of polymorphism because of highest percentage of polymorphic bands compared with the other molecular markers techniques used herein. This analysis could be a useful tool to genetic distinctiveness among cotton genotypes. This reflects the possibility of utilizing differences between cotton genotypes to improve the economical traits in cotton through the introgressions of diverse germplasm into breeding programs. Hence, the breeder could be used biochemical and molecular markers as rapid and accurate method for identification and facilitate classification of morphological traits and yield components to study germplasm management for genetic improvement of Egyptian cotton.