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Quantifying variation in animals’ paleodiet from the fossil record is difficult as a continuous record of their remains is difficult to obtain. Here we assess dietary change in seabirds from Guangjin Island, Xisha Archipelago, South China Sea, by using stable nitrogen isotopes in seabird bones and prey remains collected from a coral sand ornithogenic sediment profile. δ15N of seabird bone collagen varied from 11.7‰ to 14.1‰ (averaging 12.8‰ ± 0.4‰), but that of fish bones and scales showed minor variations. Flying fish and squid are two favorite foods of tropical seabirds, and the average values of muscle δ15N in typical flying fish and squid samples were 9.2‰ and 10.2‰, respectively. Based on nitrogen isotope mass balance calculation, we conclude that flying fish accounts for 80% ± 40% of seabird diet averaged over the past 1200 years, but this prey accounted for only about 37% ± 30% during the ‘Little Ice Age’ (AD 1400–1850). Flying fish averaged up to 88% ± 2% during the ‘Medieval Warm Period’ (AD 850–1200), close to modern observed value of 89.6%. Thus, it appears that seabirds on Guangjin Island mainly preyed on flying fish during warm periods, and shift to squid during cooler periods. Our results suggest that recent global warming and human activities have likely caused a rapid decrease in tropical seabird population and dietary shift. [ABSTRACT FROM AUTHOR]