Sea urchins play a critical role as herbivores keeping the balance between coral and algae. The White sea urchin Tripneustes ventricosus is an important herbivore of seagrass meadows along the Western Atlantic, the Caribbean Sea, and The Gulf of México. Little is known about the gut microbiota of this species using traditional microbiological methods, such as culture and microscopy. However, recent advances in molecular sequencing approaches have emerged as powerful tools to revolutionize the characterization of microbiomes in marine animals. We aim to provide insight into seasonal changes of the gut microbiota from samples of this sea urchin species at three sites of the northeastern coast of Puerto Rico, with emphasis on temporal changes, habitat effect, and size cohort effect.