Immunohistochemical analysis suggested the presence of GAMP in the exoskeleton, but GAMP could not be extracted from the exoskeleton. So, organic matrices with calcification inhibitory activity in the exoskeleton were searched, identifying calcification associated peptide (CAP)-1 and -2 from the SDS/DTT-soluble fraction. These peptides were structurally similar and had Rebers–Riddiford (R-R) consensus sequence responsible for chitin-binding and Asp-rich regions, suggesting their two roles in calcification. CAP-1 was phosphorylated at Ser70, which strengthened the calcification inhibitory activity. Examination of the structure–activity relationship of CAP-1 revealed the importance of the Asp-rich region in calcification inhibitory activity. On the other hand, from the acetic acid-soluble fraction, calcification associated soluble peptides (Casp)-1 and -2 were purified and identified. They both had R-R consensus sequence, but their chitin-binding ability was much lower than CAP-1 and -2. Casp-1 and -2 may also be associated with calcification in a similar manner to CAP-1 and -2. In addition, a matrix protein which binds to chitin extremely tightly was identified and named SCBP (strong chitin-binding protein)-1. The cDNA’s encoding all these peptides except Casp-1 were cloned, and the peptides were prepared using E. coli expression system and used for functional analyses.