The brown planthopper (BPH) is one of the most serious insects pests of rice, and the host resistance has been recognized as one of the most economic and effective measures for BPH management. In this study, we conducted a molecular-based genetic analysis of Bph9 in Kaharamana, a Sri Lanka rice variety resistant to BPH insects of East and Southeast Asia. An F2 segregating population composed of 180 plants was constructed from the cross between Kaharamana and 02428, and each F2 plant was self-crossed to obtain F2:3 family. The bulked seedling test method was used to evaluate the resistance of F2:3 families, and the genotype of each F2 plant was inferred from the phenotype of corresponding F2:3 family. Linkage analysis indicated that the resistant gene Bph9 in Kaharamana was located between SSR markers RM463 and RM5341 on chromosome 12 with linkage distances of 6.8 cM and 9.7 cM, respectively. The time- and money-saving SSR markers would be helpful in the application of Bph9 in breeding program via marker-assisted selection.