Beneficial microbial symbionts provide essential functions for their host from nutrients to defense against disease. Whether hosts acquire their symbionts directly from parents (vertical transmission) or by sampling from the environment (horizontal transmission) can have dramatic impacts on host adaptability and, in the case of ecosystem engineers, ecosystem health. Wood-boring bivalve mollusks (Teredinidae shipworms) act as ecosystem engineers in marine environments, creating habitat out of submerged wood for fish and invertebrates. Essential to shipworm success is their community of endosymbiotic gill bacteria that produce the enzymes necessary for wood digestion. How shipworms acquire their symbionts, however, remains largely unexplored. Using culturing, fluorescence in-situ hybridization, confocal microscopy, and tank experiments, we provide evidence suggesting the mode of symbiont transmission the shipworms for either the shipworm, Lyrodus pedicellatus or Teredo bartschi or both. Symbiotic bacteria were not detected by cultivation or microscopy in brooding larvae within gravid adults or as veliger larvae collected from the water column, but were observed in adult specimens and juveniles that had begun burrowing into wood. These data suggest that the specimens examined have both aposymbiotic and symbiotic life phases and acquire their symbionts through indirect horizontal transmission. Our findings reveal how the long-term brooders L. pedicellatus and/or T. bartschi acquire their gill endosymbionts.