Sea urchins are considered one of the most common benthic grazers in tropical marine ecosystems and can exert a strong in??uence in the community structure. The sea urchins Diadema antillarum, Echinometra lucunter, Lytechinus variegatus, and Tripneustes ventricosus are the most common species in the Caribbean shallow water ecosystems. Unfortunately, we lack basic knowledge of the molecular ecophysiology of these sea urchin species, particularly with respect to their bacterial microbiota. Here, we characterized the gut microbiota of four Caribbean sea urchins collected in the Northeastern coast of Puerto Rico.We compared their ecogenomic composition in di??erent niches, and in varying water temperatures to be able to project how climate change will a??ect this species. This study will thus be the steppingstone to properly understand the microbe-host interactions in this echinoderm system and how it varies with sea conditions and dietary niches. A total of 126 samples were sequenced using Illumina MiSeq and characterized QIITA and QIIME to establish a baseline bacterial pro??le of gut digesta of sea urchins within the herbivorous (seagrass) and omnivorous (coral) biotopes, inhabiting Puerto Rico shallow water