Identifying cell states during development from their mRNA profiles provides insight into their gene regulatory network. Here we leverage the sea urchin embryo for its well-established gene regulatory network to interrogate the embryo by single cell RNA-seq. We tested eight developmental stages in Strongylocentrotus purpuratus, from the eight-cell stage to late in gastrulation. We used these datasets to parse out 22 major cell states of the embryo with focus on key transition stages for cell type specification of each germ layer. Sub-clustering of these major embryonic domains revealed over 50 cell states with distinct transcript profiles. Further, we identified the transcript profile of two cell states expressing germ cell factors, one we conclude are the primordial germ cells, and the other transiently present during gastrulation. We hypothesize that these cells of the veg2 tier of the early embryo may represent a lineage that converts to the germ line when the primordial germ cells are deleted. This broad resource will hopefully enable the community to identify other cell states and genes of interest to expose the underpinning of developmental mechanisms.