A field study was carried out at the Experimental Farm of Rice Research Dept., Sakha Agricultural Research Station, ARC, Egypt through 2016 and 2017 seasons to study allelopathic activity of selected rice genotypes to integrate with herbicides use under field conditions and to assess genetic diversity using SSR markers linked to allelopathic activity. Six rice entries were used in field study included MBG-41, HHZ-12-SAL8-Y1-Y2, FFZ-1, Weed tolerant-1, Sakha 106 and non-allelopathic check Sakha 101. Pre-mixed herbicide Top Shot 6% OD (penoxsulam 1% + cyhalofop-butyl 5%) was applied at recommended and half doses as compared with untreated (weedy check) plots. Sakha 106 and Weed tolerant-1 performed the best in weed control, yield and yield attributes in both seasons, while Sakha 101 recorded the highest dry weights of studied weeds and lowest values of rice dry weight as well as grain yield and its attributes during both seasons. The recommended dose of Top Shot 6% OD was the best as compared to either half dose or untreated plots. Sakha 106 as allelopathic rice cultivar had same behavior under both recommended and half doses of herbicide in controlling grasses, sedges, broad leaves and total weeds, and produced the highest rice dry weight, grain yield and its attributes in both seasons. For molecular study, Rikuto Norin22 was used as identified allelopathic genotype. Four previously identified SSR markers linked to allelopathic activity in rice were used to study genetic diversity among studied rice genotypes. A total number of 13 alleles were generated and number of alleles per locus varied from 2 to 5. Heterozygosity (H e) values ranged from 0.490 to 0.735 with an average of 0.607. Polymorphic Information content (PIC) values ranged from 0.37 to 0.685. Genotypes were clustered based on genetic background and allelopathic activity. The results demonstrated the power of SSR markers in detecting molecular diversity as they separated indica from japonica genotypes. SSR 227 was able to detect Weed tolerant-1 and Rikuto Norin22 and Sakha106. This marker could be a potential candidate for MAS-based allelopathic selection.