The role of extracellular matrix (ECM) in the differentiation of tissue types was examined in embryos of Strongylocentrotus purpuratus. We have examined the expression of various tissue-specific molecular markers after disrupting the ECM by culturing embryos in the presence of beta-aminoproprionitrile fumarate (BAPN), which disrupts collagen deposition, and beta-D-xyloside, which disrupts proteoglycan metabolism. The markers examined included accumulation of primary mesenchyme-specific mRNA (SM 50); an aboral ectoderm-specific mRNA (Spec 1); and a gut-specific enzyme, alkaline phosphatase. Treatment with BAPN or beta-D-xyloside results in developmental arrest at the mesenchyme blastula stage. Although spicule formation is inhibited, the accumulation of SM 50 transcripts and the synthesis of most of the prominent spicule matrix proteins is similar to that of control embryos. Spec 1 mRNA, in contrast, while accumulating to a significant extent when collagen and proteoglycan metabolism is disrupted, does accumulate to a level somewhat lower than that seen in control embryos. Additionally, the postgastrula rise in gut-specific alkaline phosphatase is reversibly inhibited by BAPN and xyloside treatment. These results demonstrate a differential effect of the ECM on expression of tissue-specific molecular markers.