Organisms rely on a network of microbes that seed the host body and are maintained via a shared relationship which is often times a consortial symbiosis. Marine invertebrates, despite having highly diverse microbiomes and offering a suite of different life history traits across which to explore the members and functions of these symbionts, are largely absent from the Holobiont and microbiome literature. Here we examine how the bacterial component of the Strongylocentrotus purpuratus Holobiont (the network of dynamic interactions between the host and its microorganisms) changes in abundance and composition throughout early developmental stages. Exploring the S. purpuratus larval microbiome throughout development in the context of the sea water they live in and the algae they consume allows us to investigate not only what bacteria associate with the larvae and at what relative abundances, but also when and what bacteria may seed the microbiome via vertical transmission from gametes and via horizontal transmission through food and filtered sea water (FSW). Further understanding ontogenetic differences in the microbiome, as well as gaining new insights into when and from where marine invertebrate larval microbiomes are seeded, has important consequences for marine invertebrate aquaculture of endangered species and for ecosystem restoration and management.