This study was conducted at Regional Rice Research and Development Center ,Bombuwela Sri Lanka, to transfer two bacterial leaf blight resistance alleles to the advanced breeding line Ld 99-12-38 through back cross breeding. The transferred alleles were confirmed in BC3F2 using molecular markers. Thirty five BC3F2 progeny lines were evaluated for BLB resistance allele diversity of Xa21 and Xa4. The markers showed a length polymorphism between the resistant and susceptible lines. Out of the tested 35 progeny lines, eight were confirmed phenotypically as resistant, the lines carried the resistance alleles for the genes of interest (for both Xa21 and Xa4). In addition, twenty one lines carried only the resistant allele at Xa4, however, was phenotypically categorized as resistant/moderately resistant. A paired t-test revealed that there is a significant difference in the resistance expressed by the progeny carrying resistance alleles of two alleles than with one (p = 0.0064). it can be concluded that resistance alleles of Xa21 and Xa4 has been successfully transferred to rice lines derived from a cross between Ld 99-12-38/IRBB 60 with similer morphological characters of Ld 99-12-38.