The current gene regulatory network (GRN) of the sea urchin Strongylocentrotus purpuratus embryo describes the specification of the endomesodermal territories. However, the specification of the adjacent ectodermal territories of the embryo has been far less explored. Several recent studies on the cis-regulatory analysis of nodal and the early oral ectoderm determinants have provided clues on how the specification of this territory is initiated. Recently, a large-scale of gene regulatory network analysis was carried out in an effort to build the ectoderm specification GRN. The deduced ectodermal GRN model provides the first peek at the overall picture of ectoderm specification in the sea urchin embryo. This review integrates the current knowledge on the specification of the ectoderm by linking recent discoveries to the GRN model to understand the process of ectoderm specification in sea urchin embryos.