The present investigation was conducted at Rice Research and Training Center (RRTC), Sakha, Kafr El-Sheikh, and Laboratory of Genetics Department, Faculty of Agriculture, Tanta University, Egypt. during the three successive rice growing seasons; 2012, 2013 and 2014. Two rice varieties;SK103 and Rikuto Norin 22 as a parents of the running study and their F3, F4and F5 were evaluated against the Echinochloa crus -galli ( barnyard grass)under natural festation. The results showed that, these varieties showed biologically active suppression ofE.crus-galli under field conditions were values ranged from 2.33 to 12.6 cm for radial area and from 41.33 to 87% of weed control. The selected genotypes are important and suitable for direct seeded rice, also it could be utilized in the breeding programs to transfer allelopathic activity for commercial varieties to suppress weeds and lowering pollution. The genetic coefficient of variability refers to genotypiceffect which played an important role in the inheritance of all studied traitswere the heritability in broad sense ranged from 98.06 to 99.98 for allelopathic activity. Two of the ten tested SSR markers (Table 1); RM439 and RM164showed polymorphic DNA pattern were the primer RM164 exhibited the bandwith molecular weight 296bp in all genotypes had strong to allelopathic activity and it was absent in poor rice variety. The SSR markers would be helpful and may identify important of DNA sequencing that help in breeding program.