A wide variety of Salmonella serotypes occurs within reptilian hosts, but their ecology is poorly understood. We collected cloacal swabs from tuatara (Sphenodon punctatus), fairy prions (Pachyptila turtur), and skinks (Oligosoma spp.) on Stephens Island, New Zealand, to screen for Salmonella. Soil samples were also collected from inside burrows of tuatara and fairy prions and tested for Salmonella. We sampled repeatedly from October 2009 to October 2011. Cloacal swabs were collected from 620 tuatara, and no intestinal shedding of Salmonella was detected. Similarly, no Salmonella was detected in fairy prions. In contrast, we isolated Salmonella from 6.5% of skinks and 8.4% of soil samples. We identified two serovars of Salmonella from 52 isolates, Salmonella Saintpaul and Salmonella Mississippi. Salmonella Mississippi was isolated from skinks only and S. Saintpaul was found in skinks and soil samples. Salmonella persists in this ecosystem with skinks as the main wildlife reservoir, and an environmental reservoir exists in the soil from burrows used by skinks, tuatara, and fairy prions. Salmonella was absent from skinks and the soil in winter, raising the question of bacteria persisting through winter.