Epithelial-mesenchymal transitions (EMTs) are fundamental and indispensable to embryonic morphogenesis throughout the animal kingdom. At the onset of gastrulation in the sea urchin embryo, micromere-derived primary mesenchyme cells (PMCs) undergo an EMT process to ingress into the blastocoel, and these cells later become the larval skeleton. Much has been learned about PMC specification in sea urchin embryos. However, much less is known about how states of the sequentially progressing PMC gene regulatory network (GRN) controls the EMT process during PMC ingression. Transcriptional regulators such as Snail and Twist have emerged as important molecules for controlling EMTs in many model systems. Sea urchin snail and twist genes were cloned from Lytechinus variegates, and each has been experimentally connected to the PMC regulatory network; these experiments demonstrate several requirements for PMC ingression, and in doing so, begin to illustrate how a gene regulatory network state controls morphogenesis. Functional knockdown analyses of Snail with morpholino-substituted antisense oligonucleotides (MASO) in whole embryos and chimeras demonstrated that Snail is required in micromeres for PMC ingression. Investigations also show that Snail downregulates cadherin expression as an evolutionarily conserved mechanism, and Snail positively regulates a required endocytic clearance of epithelial membrane molecules during EMT. Perturbation experiments indicate that Twist has accessory roles in regulating PMC ingression, and possibly plays a maintenance role in PMC specification network state. In addition, Twist also functions in the post-EMT network state, particularly in directing PMC differentiation and skeletogenesis. The recently annotated sea urchin genome accelerates the discovery of new genes and holds strong promise of mapping out a complete canvas of the micromere-PMC gene regulatory network. Using the genome resources we successfully cloned several newly identified PMC genes, and found most of them to be expressed in micromeres just prior to ingression of the nascent PMCs. Current experiments focus on the roles of these genes in preparing for, executing, and/or controlling the mesenchymal behavior following PMC ingression. The functions and inter-relationships of these genes will greatly augment our understanding of how a gene regulatory network state controls a crucial morphogenetic event. / Dissertation