Diapause hormone (DH) and pheromone biosynthesis-activating neuropeptide (PBAN) code for the diapause gene (DH-PBAN) of Bombyx mori Linnaeus. The DH-PBAN gene sequence from the BLAST database was searched against B. mori genomic gene sequences for similarity. Results showed maximum homology with a genomic contig (accession no. D16230). Primers were designed for the intron, exon and promoter regions of the DH-PBAN gene sequence. The corresponding regions were amplified using genomic DNA as template and products of diapause and non-diapause silkworm races were compared. There was no variation in the 425 bp intron and 254 bp exon regions. However, 1.3% nucleotide sequence variation was observed in selected silkworm races. The promoter region showed 4.2% single nucleotide variation in the diapause and non-diapause silkworm races. The promoter region of the diapause gene showed variations in the sequence of the POU (Pit 1, Oct 1 and Unc-86)-binding site of non-diapause and diapause races of B. mori. In phylogenetic analysis, B. mori formed a cluster with other silkworms of the Bombycidae family, whereas the Noctuidae family formed a separate cluster, indicating that the diapause gene is conserved across the insect taxa.