We compared the Caribbean reef sponge, Axinella corrugata, with the Caribbean reef coral, Erythropodium caribaeorum for differences in their resident microbial communities. This cursory survey of bacterial diversity applied 16S rRNA gene sequences. Over 100 culture-independent sequences were generated from five different Axinella 16S rRNA libraries, and compared with 69 cultured isolates. The cultureindependent 16S rDNA clones displayed a higher diversity of Proteobacteria, including “uncultured” or “unknown” representatives from the Deltaproteobacteria. Arcobacterium, and Cyanobacteria were also found. We have also confirmed that Axinella sponges appeared to host specific microbial symbionts, similar to the previously identified clones termed “OSO” environmental samples. In contrast, seawater samples near Axinella were dominated by Pseudoalteromonas. Adjacent sediment samples yielded clones of Planctomycetacea, Proteobacteria, sulfate-reducing Desulfovibrio spp, and other Deltaproteobacteria. Anaerobe-like 16S rRNA sequences were detected after the oxygen supply to one Axinella sample was deliberately curtailed to assess temporal changes in the microbial community. E. caribaeorum yielded more Betaproteobacteria relative to Axinella 16S libraries, and also included the Gammaproteobacteria genus Spongiobacter. However, Axinella-derived microbes appeared phylogenetically deeper with greater sequence divergences than the coral. Overall this study indicated that marine microbial community diversity can be linked to specific source hosts and habitats.