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Long-term studies of marine communities are critical to understanding shifts in marine ecosystems in response to ecological change. We examined the diet of stranded loggerhead sea turtles (Caretta caretta) in New York waters between 1995 and 2014 using stomach content analysis, and quantified variability in loggerhead diet using Non Metric Multidimensional Scaling (NMDS). Our results provide compelling evidence for a shift in the benthic community in New York waters associated with warming temperatures. We found two distinct clusters in loggerhead sea turtle diet, comprising samples in the years before and after 2000, respectively, indicating a temporal shift in prey composition after 2000. These patterns represented a shift from larger crab species such as rock crab (Cancer irroratus) and spider crab (Libinia spp.) to smaller crab species such as hermit crabs (Pagurus spp.) in recent years. Sea surface temperature (SST) in New York waters increased during the 20-year study period, and changes in SST and the position of the Gulf Stream were the most important environmental variables explaining variability in loggerhead sea turtle diet. Our results reflect the importance of long-term data collection in evaluating ecological responses to climate-driven warming, and highlight the utility of marine vertebrates as indicators of changes to lower trophic level organisms.