Contemporary thought is that microbial communities play fundamental roles in the functioning of highly productive coral reef ecosystems. However, the dynamics governing acquisition and development of distinct microbial communities by specific coral species and individuals remains unclear. In order to provide insight into the development of specific bacterial-coral relationships, we identified microorganisms associated with major reef building corals of Hawaii in the North Pacific Ocean that represent differing modes of zooxanthellae symbiont transmission (vertical vs. horizontal), throughout the reproductive cycle, early developmental stages, and post-settlement stages of each.