Traditional techniques for stable isotope analysis (SIA) generally require sacrificing animals to collect tissue samples. In October 2018, we examined the isotopic values of fin and muscle tissue of Gymnocypris chui (n = 19) and Gymnocypris scleracanthus (n = 28) from Lake Langcuo of the Tibetan Plateau of China to determine whether non‐lethally collected pectoral fin tissue could substitute for muscle tissue in stable isotope analysis. The results showed positive relationships (r2 > 0.7) between fin and muscle tissue for both δ15N and δ13C of G. chui and G. scleracanthus. This study demonstrates the utility of a non‐lethally technique to analyze time‐integrated dietary habits and should be applicable to other fish species.