As in other rice growing locales around the world, in Kerala too, various climatic, edaphic, biological, physical, physiological and socio-economic variables impact the area, production, and productivity of the rice. Bacterial blight (BB), an important biotic stress caused by Xanthomonas oryzae pv. oryzae (Xoo) assumes a huge role in deciding rice profitability in Kerala. PTB 39 (Jyothi) and Mo 16 (Uma) are both elite rice varieties of Kerala, but extremely susceptible to the bacterial blight. Host-plant resistance is advocated as the most effective breeding strategy to combat the BB in contrast to the use of hazardous plant protection chemicals. Breeders have attempted to introgress disease resistance genes (R-genes) into rice cultivars to impart BB resistance. Markerassisted selection (MAS) enables pyramiding multiple R-genes along with rapid background recovery of the recurrent parent, while maintaining the exquisite quality characteristics of rice.Considering the impact of the disease on food security and sustainability, efforts to introgress three R-genes (xa5, xa13 and Xa21) into the variety Jyothi from donor parent Improved Samba Mahsuri (ISM) through MAS were made. Foreground selection of the BC₂F₄ individuals was done using the Sequence Tagged Sites (STS) as well as functional markers. Foreground selection of the BC2F4 individuals was done using the xa5 gene linked STS marker RG556. Restriction digestion of the PCR product of the STS marker with Dra1 restriction enzyme, resulted in production of alleles of size 238bp and 438bp in all the BC₂F₄ individuals including the parents, indicating the presence of R-gene xa5. Amplification of DNA of the individuals with the functional marker xa5SR further confirmed the presence of R-gene xa5 in the parents as well as in the 51 BC₂F₄ individuals. Foreground selection with STS marker pTA 248 to detect the presence of Xa21 gene revealed that in BC₂F₄ Plant No. 9 and plant no. 21 amplicon of size 992 bp, as found in the donor parent ISM was present. And background selection was done by using rice microsatellite (RM) simple sequence repeats (SSR) markers.