Characterizing patterns in the microbial communities that dwell within key species is critical to understanding the role of microbes in shaping fundamental aspects of marine ecosystems. Sea urchins are key grazers in coastal seas, where they can survive a variety of conditions and diets, enhancing their ecological impact on kelp forests. Here we provide the first evidence that the two dominant sea urchin species in southern California have distinct gut microbiomes that vary with habitat. The taxonomic composition of the urchin microbiomes suggests that they may facilitate digestion of food and be a source of nutrition themselves. More work is needed to understand the extent to which their microbiome is the key to sea urchins' ecological success.