The ecological and evolutionary forces that shape interactions between marine sponges and their symbiotic microbiota remain poorly understood. Considerable work has been done to characterize the sponge microbiome, and this research has shown that there are two distinct types of sponges: those with high microbial abundances (HMA) and those with low microbial abundances (LMA). There is no clear evolutionary driver for this distinction, and we have only a limited understanding of how HMA or LMA status affects host phenotypes (e.g. feeding behavior, capacity for nutrient cycling). We had two primary goals with the present study. First, we used a variety of microscopic techniques to compare aspects of host biology (e.g. choanocyte chamber morphology and density) in the context of symbiont status. Secondly, we used molecular approaches to uncover components of ecological structure of bacterial communities in HMA versus LMA sponges (e.g. species richness, evenness). We found that choanocyte chamber density is greater in LMA sponges than in HMA sponges. We also found distinct patterns of organization for bacterial communities in HMA and LMA sponges, although environmental factors, to a lesser degree, also influence community structure in the Floridian sponges we examined. These results suggest that the large bacterial communities found in HMA sponges may allow the host to decrease their heterotrophy versus that of LMA sponges with minimal bacterial communities.