Sea urchins are important inhabitants of many marine ecosystems. They are also an economic resource for many international fisheries and are an important animal model in developmental biology. Sea urchins ingest a variety of plant and animal matter, form a digesta pellet, and produce an egesta (fecal) pellet that contributes to benthic food webs. The size and morphology of fecal pellets produced by various size classes of the sea urchin Lytechinus variegatus fed a variety of natural, vegetable-based, or formulated diets were characterized in terms of two-dimensional area, length (long diameter), width (short diameter), and circularity, as well as by ultrastructure analysis using transmission electron microscopy (TEM). Sea urchins fed natural and vegetable-based ingredients produced a wide variety of irregularly shaped egesta that were loosely surrounded by mucus, whereas urchins fed a formulated diet produced highly circular egesta surrounded by a uniform multilayered mucus coat. Larger urchins (62 ± 3.1 g wet weight) consuming a formulated diet produced egesta that were larger in size than smaller adult (26.5 ± 2.7 g) or juvenile urchins (3.6 ± 0.4 g), with egesta length of 0.93 ± 0.06, 0.75 ± 0.05, and 0.61 ± 0.01 mm, respectively (mean ± 95% confidence interval [CI]; P < 0.001). Ultrastructural analysis of the egesta using TEM image analysis software from urchins consuming formulated diets indicated that pellets contained extensive bacterial communities, ranging from 31% to 69% of the total cross-sectional area of the pellet, with dense communities located near the surface of the pellet (9.51 × 10⁸ cells/cm²). Qualitative examination of the egesta TEM suggested the presence of a diverse bacterial community. Following egestion, these microbial communities are suggested to have an important role in natural food webs, with potential value for integrated multitrophic aquaculture systems.