The brown planthopper, Nilaparvata lugens is a pest of cultivated rice throughout Asia and is controlled using insecticides and/or resistant rice varieties. This species has developed resistance to many classes of insecticide and biotypes have developed that are virulent against formerly resistant rice cultivars. Insects use a suite of detoxification enzymes, including cytochrome P450s, glutathione S-transferases and carboxyl/cholinesterases to defend themselves against plant secondary metabolites and pesticides. Pyrosequencing on the Roche 454-FLX platform was used to produce a substantial expressed sequence tag (EST) dataset to complement the existing Sanger sequenced ESTs in GenBank. A total of 78959 reads were combined with the 37392 publically available Sanger ESTs; these assembled into 8 911 contigs and 10620 singletons. Analysis of the distribution of tentative unique genes (TUGs) with the gene ontology for biological processes and molecular functions suggests that the 454 and Sanger EST assembly is broadly representative of the N. lugens transcriptome. The brown planthopper transcriptome was found to contain 31 TUGs encoding P450s, nine encoding glutathione S-transferases and 26 encoding carboxyl/cholinesterases and many of these are putatively involved in the detoxification of xenobiotics. The Agilent eArray platform was used to construct an oligonucleotide microarray populated with probes for ∼19000 unigene sequences, including all those known to encode detoxification enzymes. The genomic resources developed in this study will be useful to the community studying this crop pest and will help elucidate the molecular mechanism underlying insecticide resistance and planthopper adaptation to resistant rice cultivars.