We collected flying fish (Exocoetus volitans) from the South China Sea to determine whether fish scale isotope values correlate with those from muscle, and discuss relevant eco-environmental implications. A significant positive correlation was determined between fish scales and muscle δ13C and δ15N, rendering a fish scale an alternative to muscle tissue for stable isotope analysis. However, muscle and scale isotopic offsets should be fully considered when using δ13C and δ15N to analyze the actual trophic level of fish and their food source. The average offsets of δ13C and δ15N between muscles and scales are-2.1 ± 0.5‰ and 2.3 ± 0.6‰, respectively, though these values vary slightly with fish mass. Weak correlations were found between δ13C and δ15N, both in the flying fish muscle and scales, suggesting that other factors are influencing δ13C and δ15N. Fish δ15N also correlates with the size of individuals, while δ13C reflects the marine habitat. Based on our data, it appears that more eco-environmental processes can be revealed from modern or ancient flying fish scales.