High-resolution genetic linkage maps are becoming increasingly important in genetic and genomic studies. In this study, several methods were used to construct a high-resolution linkage map for the brown planthopper. In addition to previously identified markers, a number of new SSRs mined from transcriptome databases within our group were developed and SRAP markers were also used for the first time in N. lugens. Overall, 2144 unique markers were considered in this work, of which 966 were informative for map development. The information provided by these molecular markers represents a valuable resource for genetic and genomic studies on this insect. Three populations were analyzed in the construction of the map. Brown planthoppers are known to exhibit high levels of heterozygosity, and the number of successful progeny per mating is limited. We therefore constructed a consensus linkage map by integrating information from multiple families. Comparing to previous genetic map of this insect, the basic characteristics was significantly improved in this map. First, it consists of 15 linkage groups that coincide with the species’ 14 autosomes and one X chromosome. Conversely, the map developed by Jairin et al. features 17 linkage groups. In total, 283 of the markers used in Jairin’s map were incorporated into our consensus map. As a result, we were able to combine LG9 and LG16 from the Jairin’s map into a single group corresponding to chromosome 8, and to combine the Jairin’s linkage groups LG15 and LG17 into a group corresponding to chromosome 12. Unfortunately, additional markers will be required to construct a linkage map for the Y chromosome. According to their length in cM, to these 15 linkage groups, which should greatly facilitate studies hereafter. We numbered the linkage groups based on their lengths in cM, which should greatly facilitate future studies using our map. The map spans 956.6 cM, which corresponds to 96.6% of the estimated size of the N. lugens genome. It is based on 886 molecular markers with an average distance between adjacent markers of 1.1 cM. Such high density maps covering the whole genome of the target species are valuable tools for dissecting the genetic basis of important traits. Another prominent merit of our molecular map is the use of gene-specific markers as anchors on each chromosome. On average, there are eight anchor markers per chromosome. The sequences from which the markers were developed are over several hundred bases in length and are known to correspond to a specific protein or gene. These markers function as chromosomal landmarks, especially when they cluster together. For example, the vitellogenin gene on the X chromosome was previously located on the sex linkage group in previous maps. However, based on our map, we were able to demonstrate that the transposase-like protein and death-associated protein are also located on this chromosome.