In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinusvariegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstreambioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance ofCampylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- andEpsilonproteobacteria at approximately equal capacities. The gut digesta and egested fecal pellets exhibited a microbialprofile comprised of Gammaproteobacteria, mainly Vibrio, and Bacteroidetes. Both the seagrass and surrounding sea waterrevealed Alpha- and Betaproteobacteria. Bray-Curtis distances of microbial communities indicated a clustering profile withlow intrasample variation. Predictive metagenomics performed on the microbial communities revealed that the gut tissuehad high relative abundances of metabolisms assigned to the KEGG-Level-2 designation of energy metabolisms comparedto the gut digesta, which had higher carbohydrate, amino acid and lipid metabolisms. Overall, the results of this studyelaborate the spatial distribution of microbial communities in the gut ecosystem of L. variegatus, and specifically a selectiveattribute for Campylobacteraceae in the gut tissue. Also, the predictive functional significance of bacterial communities inuniquely compartmentalized gut ecosystems of L. variegatus has been described.