Cloning-based approach combining homology search in the Bombyx genome sequence and Rapid Amplification of cDNA Ends (RACE) resulted in annotation of 23 neuropeptide genes and different splicing variants of three genes. In total 37 neuropeptide genes in addition to bombyxin gene family have been identified in Bombyx. Comparison of available insect neuropeptide genes revealed that the silkworm genome contains most conserved neuropeptide genes except those encoding proctolin, vasopressin-like peptide and neuropeptide-like precursor 2. In addition, we identified several paralogous neuropeptide genes which have not been found in other insects. The Bombyx genome contains a triplet of paralogous genes encoding adipokinetic hormones (AKH), two genes encoding different neuropeptide Fs (NPFs) and a tandem of related SIFamide and IMFamide genes. A novel gene coding for CCHamide was cloned and its expression in the CNS and midgut was demonstrated. Differential splicing was observed for the first time in transcripts for diuretic hormones and cardioacceleratory peptides 2b. Most paralogous genes or splicing variants of the same gene showed different expression patterns in the central nervous system (CNS). These results suggest that unique duplication and differential expression of several neuropeptide genes occurred during the evolution in Bombyx. This may be an effective mechanism for functional diversification of conserved neuropeptides.