In southern Louisiana, high population densities of exotic Myocastor coypus (Nutria) have been implicated in causing significant coastal marsh damage through extensive herbivory. Wildlife officials instituted a Nutria removal program in 2002 to reduce this marsh loss. Because Alligator mississippiensis (American Alligator) frequently consume Nutria, concern arose regarding the program's impacts on alligator food habits. Therefore, we conducted our study to determine if the Nutria removal program affected the frequency of occurrence of Nutria remains in alligator stomachs collected from five parishes in southern Louisiana. Three parishes had high Nutria densities and removal programs; two parishes had low Nutria densities and no Nutria removal. We collected >550 alligator stomachs during three September trapping seasons and examined the contents of each. We used logistic regression to model effects of year (1 year prior to the removal program compared to two years during removal) and parish (three with Nutria removal programs compared to two without) on the probability that an alligator stomach contained Nutria remains. Overall, about one-third of the alligator stomachs contained Nutria remains. Nutria removal appeared to have no effect on the probability of a stomach containing Nutria remains even after two years of Nutria removal. In addition, the probability that an alligator stomach contained Nutria remains was similar among all parishes regardless of whether Nutria removal occurred or not. We recommend that continuance of the Nutria removal program be based on its effectiveness in reducing marsh damage and not on perceived impacts to alligator food habits.