AbstractBackgroundModerate to high DDT resistance in generally associated with overexpression of multiple genes and therefore has been considered to be polygenic. However, very little information is available about the molecular mechanisms that insect populations employ when evolving increased levels of resistance. The presence of common regulatory motifs among resistance‐associated genes may help to explain how and why certain suites of genes are preferentially represented in genomic‐scale analyses.ResultsA set of commonly differentially expressed genes associated with DDT resistance in the fruit fly was identified on the basis of genome‐wide microarray analysis followed by qRT‐PCR verification. More genes were observed to be overtranscribed in the highly resistant strain (91‐R) than in the moderately resistant strain (Wisconsin) and susceptible strain (Canton‐S). Furthermore, possible transcription factor binding sites that occurred in coexpressed resistance‐associated genes were discovered by computational motif discovery methods.ConclusionA glucocorticoid receptor (GR)‐like putative transcription factor binding motif (TFBM) was observed to be associated with genes commonly differentially transcribed in both the 91‐R and Wisconsin lines of DDT‐resistant Drosophila. © 2012 Society of Chemical Industry