Abstract: The aim of present study was to identify the genetic locus associated with brown planthopper resistance in rice. We studied the response of segregating population (F3) from cross between the susceptible popular indica variety Swarna and the resistant variety PTB33 for its reaction against Indian biotype of BPH. A population comprising of 106 F3 families along with their parents and the resistant (PTB33) and susceptible check Taichung Native1 (TN1) were evaluated for BPH resistance at seedling stage using the standard seed box method. The results indicated the presence of dominant gene controlling the resistance. Linkage analysis with SSR markers through bulked segregant analysis method was employed for the identification of DNA markers linked to the resistance genetic locus. Single-marker analysis through one way analysis of variance with crop stat showed that the markers RM3766, RM14687, RM251 and RM7 on chromosome 3 were linked to the resistance locus. Further study led to the identification of markers RM3766 and RM14687 linked to a major QTL associated with BPH resistance physically mapped on short arm of chromosome 3. This QTL showed an additive effect of 0.7 and dominance effect 0.3. The identified QTL on chromosome 3 is new source of resistance derived from the resistant parent PTB33.