Herbivores are challenged when selecting a diet because many plants have limited nutritional value and some use defenses to avoid being eaten. Understanding diet selection of herbivores in most landscapes also involves choices between native versus nonnative plant species which, in turn, informs management actions to conserve the species. The New England Cottontail, Sylvilagus transitionalis (Bangs 1895)—a species on the decline—is the focus of a large conservation consortium. We conducted microhistological analyses of feld collected fecal samples and feld surveys of plant species available to determine winter diet of New England cottontails on Patience Island, Rhode Island. Energy density (total nitrogen, crude fat, energy, neutral detergent fber, acid detergent fber, ash, and total phenolics) was measured for each of the available plants. A used-available framework was used to determine the selection of each species identifed in their feces and how this related to the measured nutritionally relevant constituents. We hypothesized that New England cottontails would select plant species with higher protein and energy values and select native versus nonnative plant species. Unexpectedly, New England cottontails did not select plants with higher protein or energy content but rather plants with higher phenolic and ash levels. In addition, New England cottontails strongly selected native plant species. Our results support previous research that New England cottontails are generalist herbivores, but that plant defences and whether the plants are native play a role in diet selection.