In the USA, sea urchin aquaculture is in its infancy. One concern with current captive culture involves maintaining roe, or "uni," quality. Diet of cultured urchins has been shown to affect roe quality. Sea urchins have a unique digestive system and lack certain digestive enzymes, yet they are able to digest high percentages of food biomass consumed. It is hypothesized that their highly efficient digestion is because of the presence of bacteria in the gut. This study determined bacterial profiles in guts of captiveraised sea urchins, Lytechinus variegatus, by analyzing DNA extracted from the urchins. Using a bacteria-specific forward and universal reverse primer, 16s rDNA genes were amplified using L. variegatus gut DNA samples and subsequently cloned. Recombinant colonies containing putative 16S rDNA were randomly selected for sequencing. Sequences generated from these clones were analyzed and compared with published bacterial 16S rDNA sequences available through the National Center for Biotechnology Information database. Sequence data analysis suggested that the captive-raised sea urchins contained a limited number of representative genera. The genera most commonly identified included Pseudomonads, Vibrio, and various epsilon and gamma proteobacterium species. © by the World Aquaculture Society 2010.