AbstractReproductive isolation between different host populations is often based on intraspecific sex pheromone differences. The mechanisms underlying these differences have not been thoroughly elucidated to date. Previous studies suggested that Chilo suppressalis has differentiated into rice and water-oat host populations, and these two populations manifest clear differences in sex pheromone titer and mating rhythm. Hence, this moth is an ideal model to investigate the endogenous mechanisms of intraspecific reproductive isolation. Here, we identified a series of putative genes associated with sex pheromone biosynthesis based on the C. suppressalis pheromone gland transcriptome data. Transcripts of most genes were at higher level in the rice population. Then we obtained 11 pivotal differentially expressed genes (DEGs). The expression levels of these DEGs exhibited a distinct increase in the rice population. Moreover, we also observed the expression rhythm of these DEGs is discrepant between two host populations. Our study offers a new understanding to elucidate the mechanisms of intraspecific reproductive isolation.