The use of SRAP markers increases the density of linkage maps and also enables the identification of functional markers. In this work, 106 primer combinations including 25 forward and 36 reverse primers were used in the linkage analysis of the F2 population. 200 SRAP polymorphic loci were generated, giving an average of 1.89 polymorphic loci per primer combination. In total, 966 informative SSR and SRAP markers were used to genotype individuals from the three mapping populations. A segregation analysis was performed, and those markers that were found to be distorted were excluded from subsequent analyses. This left 707 markers for use in the F2 mapping population, 302 in the F1 population, and 305 in the F1 population. A consensus linkage map was constructed based on the loci that were common to all three or two populations by using the “combine groups for map integration” function of the JoinMap 4.0 program. The consensus molecular map contained 886 markers with 868 unique positions in 15 linkage groups, which matches the brown planthopper’s haploid chromosome number. Based on their lengths in the consensus map, the linkage groups were designated Chr1-Chr14 and ChrX corresponding to the X sex chromosome. The characteristics of the consensus map are summarized in Table 2, and the distributions and positions of the markers across linkage groups are shown in Figure 3 and Table S7. In summary, this molecular linkage map of brown planthopper spanned 956.6 cM in total, covering 96.6% of the species’ estimated genome size. The lengths of individual linkage groups ranged from 26.0 cM for the shortest to 87.5 cM for the longest. The linkage group with the greatest marker density was Chr11, with an average distance between markers of 0.71 cM. Those with the lowest marker densities were Chr1 and Chr3, for which the average distance between markers was 1.82 cM. Across the whole map, there were only 6 cases in which the distance between adjacent markers was greater than 10 cM; the largest gap was on ChrX and extended over 12.2 cM. The number of markers per linkage group ranged from 29 to 83, with an average of 59 markers per group. The new consensus map thus provides greatly enhanced marker density and resolution compared to that available previously. The use of gene-based markers made it possible to map genes with known functions onto the new linkage map. Public databases were searched to identify genes and proteins of known function corresponding to the 322 EST sequences and the 357 associated EST-SSRs. No BLAST hits could be identified for the shorter EST sequences. However, 110 EST sequences corresponding to 124 EST-SSRs were matched to proteins or genes of known function with E values of,1025. These gene-specific SSRs were used as anchor markers for each chromosome. The number of gene specific markers per chromosome ranged from 3 to 15, with an average of 8.