The developing sea urchin embryo forms endoskeletal CaCO3 containing spicules which are elaborated by the primary mesenchyme cells, descendants of the micromeres, beginning at gastrulation. In this and the accompanying paper [H. M. Sucov, S. Benson, J. J. Robinson, R. J. Britten, F. Wilt, and E. H. Davidson (1987) Dev. Biol. 120, 507-519] the isolation and characterization of a gene that encodes a 50-kDa spicule matrix glycoprotein that we call SM50 are described. A cloned cDNA isolated from a lambda gt11 library was used in hybrid-selected translation and hybrid arrest of translation experiments to verify that the cDNA encodes a spicule matrix protein. The cognate RNA transcript encodes a 50-kDa protein which is precipitated by polyclonal antisera against spicule matrix proteins and is present only in polyadenylated RNA at stages known to be making a spicule. The cloned cDNA sequence described in the accompanying paper was used to follow the time of expression of the cognate gene by RNA blotting analysis. The 2.2-kb mRNA is first detected at late cleavage stages and rapidly accumulates as the primary mesenchyme forms, reaching an apparent maximum concentration in the late gastrula and pluteus stages. The cDNA was also used to identify the cells that contain the transcripts by hybridization in situ. Hybridization to cellular transcripts is first detected in primary mesenchyme cells as they enter the blastocoel, and transcripts are confined to these cells during spicule formation and subsequent development.