The silkworm, Bombyx mori, is an important economic insect for silk production. However, many of the mature peptides relevant to its various life stages remain unknown. Using RP-HPLC, MALDI-TOF MS, and previously identified peptides from B. mori and other insects in the transcriptome database, we created peptide profiles showing a total of 6 ion masses that could be assigned to peptides in eggs, including one previously unidentified peptide. A further 49 peptides were assigned to larval brains. 17 new mature peptides were identified in isolated masses. 39 peptides were found in pupal brains with 8 unidentified peptides. 48 were found in adult brains with 12 unidentified peptides. These new unidentified peptides showed highly significant matches in all MS analysis. These matches were then searched against the National Center for Biotechnology Information (NCBI) database to provide new annotations for these mature peptides. In total, 59 mature peptides in 19 categories were found in the brains of silkworms at the larval, pupal, and adult stages. These results demonstrate that peptidomic variation across different developmental stages can be dramatic. Moreover, the corpora cardiaca-corpora allata (CC-CA) complex was examined during the fifth larval instar. A total of 41 ion masses were assigned to peptides.