Caribbean mangrove-associated sponge communities are very distinct from sponge communities living on nearby reefs, but the mechanisms that underlie this distinction remain uncertain. This study aimed to elucidate the relative importance of substrate and habitat in determining the ability of sponges to persist in mangrove ecosystems, and to evaluate the role of bacterial symbiont composition and carbon uptake in sponge distribution. Two reef species (Aplysina archeri and Desmapsamma anchorata) were transplanted to mangrove roots and PVC tubes at a mangrove stand and a reef site. The mangrove species Mycale microsigmatosa was transplanted to both substrates in mangroves as control and showed complete survival. In contrast, lowest survival for D. anchorata was observed on roots in mangroves and intermediate survival on both PVC in mangroves and roots on the reef. Complete survival was observed on PVC on the reef. A. archeri had reduced survival in all treatments, but was most affected by the root substrate in mangroves. These results reveal that the inability of typical reef species to survive in mangrove ecosystems is related to habitat and substrate. The symbiotic bacterial communities were host specific and very similar before and after transplantation. The cluster analysis of metabolic diversity of bacterial communities in A. archeri, M. microstigmatosa and D. anchorata showed strong separation between host species and the surrounding water. It is speculated that compositional differences in dissolved organic matter (DOM) composition and symbiotic bacteria are potentially important in structuring sponge communities, explaining the exclusion of typical reef species and persistence of mangrove species in mangrove ecosystems. © Inter-Research 2013.