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The increased use of chemicals in rice farming poses significant issues regarding the emergence of pesticide/fungicide resistance and environmental sustainability concerns. This study was aimed at the genetic improvement of blast, bacterial leaf blight (BB) and gall midge resistance in a popular rice variety CO 51 which already harbours a blast resistance gene <i>Pi54</i>. Efforts were made to pyramid an additional blast resistance gene <i>Pi9</i> along with two BB resistance genes (<i>xa13</i> and <i>Xa21</i>) and two gall midge resistance genes (<i>Gm1</i> and <i>Gm4</i>) into an elite rice variety CO 51 to enhance the resistance level to biotic stresses. The superior lines were selected using functional markers conferring resistance to blast (NBS4 and Pi54MAS linked to <i>Pi9</i> and <i>Pi54</i> genes, respectively) and BB [(<i>xa13Prom</i> (<i>xa13</i>) and pTA248 (<i>Xa21</i>)] and SSR markers linked to <i>Gm1</i> (RM1328) and <i>Gm4</i> (RM22550) for phenotypic screening and agronomic evaluation. The genotyping and phenotyping of F₆ and BC₂F₆ progenies of CO 51 X 562-4, for agronomic traits and resistance to BB and blast, identified ten superior progenies in F₆ and five superior progenies in BC₂F₆. The breeding lines harbouring both <i>xa13</i>+<i>Xa21</i> exhibited high levels of resistance to BB (score ≤ 1 cm) and <i>Pi9</i>+<i>Pi54</i> exhibited strong resistance to blast (score ≤ 2). Identified lines can be evaluated further for varietal improvement or utilised as genetic stocks in breeding programs.