The pheromone biosynthesis in Plutella xylostella is more active in the scotophase than in the photophase, indicating that there may be changes of gene expression in the pheromone glands. To identify genes contributing to change in pheromone production, we analyzed transcriptomes of pheromone glands from both decapitated females (PG-minus) in the photophase and normal ones (PG-plus) in the scotophase. Deep sequencing for mRNAs in the pheromone gland yielded approximately 7.5Gb and 6,671 transcripts showing positive FPKM value were analyzed. Differentially expressed gene analysis revealed that up- and down-regulated transcripts were 310 and 326 in the PG-plus transcriptome, respectively. Genes putatively involved in the pheromone biosynthesis pathway were identified such as acetyl-CoA carboxylase, acetyl-CoA dehydrogenase, fatty acid synthase (FAS), desaturases (Δ9 and Δ 11) and fatty acid reductases of pheromone gland (pgFAR), alcohol oxidase, aldehyde oxidase and aldehyde reductase, etc. Quantitative RT-PCR revealed that expressions of FAS, Δ11 desaturase and pgFAR were significantly higher in PG-plus, suggesting that they may have crucial roles in sex pheromone biosynthesis of P. xylostella