Coccoliths produced by unicellular coccolithophore algae are known as their beautiful shape and geological importance in the earth history. Coccoliths are arranged on the cell surface by exocytosis after completion of formation in the coccolithosome in the cell. An acidic polysaccharide, CMAP, was identified as organic matrix with calcification inhibitory activity. CMAP is a polymer with a unit consisting of L-iduronic acid, meso-tartaric acid, and glyoxylic acid. In Pleurocrysis carterae, coccolith is formed at the peripheral area on the base plate made of cellulose. We identify a protein named CSAP-2 extremely tightly bound to the base plate and possibly inducing the initiation of coccolith crystallization. On the other hand, natural and artificial coccolith-deficient mutants were obtained, and genes whose expression was much less than that of wild type alga were searched by suppressive subtractive hybridization (SST), resulting in obtaining two candidate genes, st-1 and st-2. Of the two genes, st-2 was found to be expressed in accordance with coccolith formation.