Genes encoding reverse transcriptase, calcium calmodulin-dependent protein kinase, replication protein and pre-mRNA-splicing factor were mapped to the Chr2 linkage group. These genes are important for essential cellular functions. The genes mapped to the Chr3 linkage group included those encoding guanine nucleotide exchange factor and cell division cycle-associated protein. Six different EST-SSRs associated with the gene encoding methionine-R-sulfoxide reductase were identified in the Chr4 linkage group. While some of these SSRs were located in close proximity to one-another, others were more widely separated. This may reflect the presence of large introns in this gene. A gene encoding anacetylcholinesterase was also mapped to this chromosome. Markers for the acetylcholinesterase gene and genes encoding zinc finger proteins were mapped to the Chr5 linkage group. Linkage group Chr6 was associated with genes encoding microtubule-associated protein and pyridoxine pyridoxamine 5phosphate oxidase. The brown planthopper genes encoding neuropeptide GPCR A5 and cytochrome P450 CYP6ER1 were mapped to linkage group Chr7, along with markers associated with EBNA2 binding protein p100 and ribosomal proteins. Linkage group Chr8 featured markers associated with the mucinlike protein gene, which may be important for the feeding behavior of brown planthoppers. Markers associated with histone RNA hairpin-binding protein, silencing protein and cysteine proteinase inhibitor precursor were mapped to the Chr9 linkage group. The Chr10 linkage group contained two markers for cytochrome P450 CYP6ER1, while the Chr11 linkage group contained 15 gene-specific annotated SSRs corresponding to the actin and chitin deacetylase genes. The EST-SSRs of the Chr12 linkage group were associated with chromodomain-helicase-DNAbinding protein and angiotensin converting protein. The Chr13 linkage group contained three EST-SSRs corresponding to the tyrosine-protein phosphatase gene. Only 3 gene-specific SSRs were anchored in the linkage group Chr14, corresponding to the gene for ESF1-like protein. Finally, 10 EST-SSRs corresponding to the vitellogenin gene were identified in the ChrX linkage group, along with markers for the transposase-like protein and deathassociated protein genes. We have constructed the most comprehensive linkage map for N. lugens that is currently available and demonstrated that brown planthopper virulence towards rice plants is controlled by a small number of genetic loci. To the best of our knowledge, this is the first study to successfully locate virulence factors in the genome of this important agricultural insect by marker-based genetic mapping. Building on the previous results, we constructed a high density molecular linkage map for the brown planthopper genome in order to enable the mapping of specific genes. The loci governing host preference and growth rate were delimited to specific regions flanked by molecular markers.