BackgroundMarine invertebrate-associated microbial communities are interesting examples of complex symbiotic systems and are a potential source of biotechnological products.ResultsIn this work, pyrosequencing-based assessment from bacterial community structures of sediments, two sponges, and one zoanthid collected in the Mexican Caribbean was performed. The results suggest that the bacterial diversity at the species level is higher in the sediments than in the animal samples. Analysis of bacterial communities’ structure showed that about two thirds of the bacterial diversity in all the samples belongs to the phyla Acidobacteria and Proteobacteria. The genus Acidobacterium appears to dominate the bacterial community in all the samples, reaching almost 80% in the sponge Hyrtios.ConclusionsOur evidence suggests that the sympatric location of these benthonic species may lead to common bacterial structure features among their bacterial communities. The results may serve as a first insight to formulate hypotheses that lead to more extensive studies of sessile marine organisms’ microbiomes from the Mexican Caribbean.Electronic supplementary materialThe online version of this article (doi:10.1186/0717-6287-47-67) contains supplementary material, which is available to authorized users.