Development of some animals is influenced by and, in some cases, dependent on the associated microbiota. The timing of when associated bacterial communities are established during the development of marine invertebrates and their subsequent dynamics across stages are known for only a few species. Here, we compared the bacterial communities of 3 confamilial echinoids from egg to juvenile using sequence-based approaches. Bacterial communities are established on unfertilized eggs and change gradually during embryonic and larval development. Despite the differences amongst these pre-metamorphic stages, approximately 30% of operational taxonomic units (OTUs) identified in association with unfertilized eggs were present in the juveniles. During embryonic development, host-associated communities diverged from the environmental microbiota but later converged following the onset of larval feeding. Taken together, the data presented here support the hypothesis that bacterial communities are established prior to fertilization and community composition shifts gradually thereafter, all the while remaining distinct from the environment. Future work will need to determine the relative influence of the host and bacteria–bacteria interactions in shaping the associated bacterial community to more broadly determine the potential functional importance of bacteria during the development of larval sea urchins and benthic marine invertebrates.