The benefits of mutualistic associations between prokaryotes and their eukaryotic hosts lead to the evolution of adaptations that encourage the relationship in subsequent generations of the host. Symbiont-dependent host reproduction may play a key role in the maintenance of the association and persistence of the microbial symbiont in the host population. Recently, sexual reproduction in the marine bryozoan, Bugula neritina, was reported to be influenced by its defensive symbiont, “Candidatus Endobugula sertula”. It was proposed that the symbiont-produced predation-deterrent compound acts as a signal to affect female reproductive processes in the host colony. An anatomical comparison of female reproductive structures and oogenesis between symbiotic and symbiont-reduced colonies was performed. Colonies of two cryptic species of B. neritina, Type S and N, were collected in North Carolina and Virginia, USA over several seasons November 2014–December 2015. Relative expression of genes regulating the female reproductive processes in the host was also assessed. Interestingly, no anatomical or molecular differences were found although there were fewer sexual zooids in symbiont-reduced colonies. The lack of difference in oogenesis indicates that the symbiont does not affect female structures and functions in the zooid, but potentially influences early differentiation of female germinal cells. Histological investigation revealed previously undescribed ‘funicular bodies’ containing bacteria in the symbiotic colonies. However, the bacteria associated with the ‘funicular bodies’ and funicular strands in the symbiotic colonies were morphologically different, thus raising the question if the symbiont exists in pleomorphic forms depending on the tissue environment it is localized.