Morphogenesis in sea urchin embryo provides excellent model system for understanding molecular role of extracellular matrix (ECM) in multi-cellular animals. Sea urchin embryonic cells are surrounded by apical and blastocoelic ECM. These ECM components provide not only essential scaffold for morphogenetic movements, such as cell migration, cell differentiation, epithelial invagination and protrusion, but also as source of cell signaling molecules, such as growth factors. The apical surface of embryo is coated with numerous large molecules, including collagen laminin, fibropellins, hyalin, and pamlin in addition to sulfated glycosaminoglycans. The blastocoelic and basal lamina ECM comprised of collagen, fibronectin-like protein, pamlin, and sulfated glycosaminoglycans, such as heparan sulfate and dermatan sulfate. Primary mesenchyme cell (PMC) ingression is the first visual indication of the onset of morphogenesis. PMC express epithelial cell surface-specific protein (Epith) until immediately before ingression. However, during PMC ingression period Epith protein [1] and cadherin [2] internalized only among presumptive PMC in the ectoderm, losing an ectodermal cell surface specificity. On the contrary, PMC present P4 a new cell surface protein, during same period. Both cell surface protein presentation and internalization require non–receptor type protein tyrosine kinase activity that is independent of ECM signaling mechanism. For PMC migration in the blastocoel, pamlin is an essential molecule in the basal lamina that navigates the direction of PMC migration. Pamlin binds to growth factor receptor-like proteins, such as FR-IR protein, an RGDS-binding protein, in the plasma membrane in vitro, and triggers activation of cytoplasmic phosphorylation signal transduction pathways in PMC, including SUp62 protein, a dimeric protein in the cytoplasm that is phosphorylated at tyrosine residues [3], and ERK ½ that ends up with myosin light chain phosphorylation and cell migration. The growth factor-mediated signal transduction also contributes to gastrulation by promoting cell proliferation at vegetal pole ectoderm that is a main reservoir of cells for archenteron elongation. Another major morphogenetic movements, such as spiculogenesis and pigment cell differentiation are also at the down stream of MAP kinase pathway.