Since small prairie mammals, such as voles and mice, strongly affect prairie plant communities, understanding their roles in restored (planted) and remnant prairies is of value. We used stable isotope ratios of carbon and nitrogen in fur samples of live trapped prairie mammals to explore their diets. Fur serves as a record of diet across months and provides a broad snapshot of the degree to which individuals are consuming C3 and C4 plants and the amount of animal matter in their diet. We used and compared two approaches, namely linear mixed random effects models and the integration of stratified random sampling and multilevel models, to increase the validity of our results. Together our analyses suggested significant differences in the isotope ratios of carbon for voles and mice and differences in nitrogen between individuals inhabiting restored as compared to remnant prairies.