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<i>Hypophthalmichthys nobilis</i> are widely distributed in the Yangtze River basin and its related lakes. They are an important economic fish species and are a famous cultured species known as the “Four Famous Domestic Fishes” in China. Currently, with the fishing ban in the Yangtze River basin, fishing for <i>H. nobilis</i> in the natural water bodies of the Yangtze River basin has been completely prohibited. In order to identify the sources of <i>H. nobilis</i> appearing in the market, further control and accountability is necessary to trace the sources of <i>H. nobilis</i> in the Yangtze River basin and its related water bodies. Therefore, this study identified and traced different sources of <i>H. nobilis</i> through muscle element fingerprint analysis (EFA). The results show that <i>H. nobilis</i> from different stations have characteristic element compositions. The characteristic element of <i>H. nobilis</i> from Wuhan (WH) is Pb, which is significantly higher than that in other stations; the characteristic element from Anqing (AQ) is Hg, which is significantly higher than that in other stations; and the characteristic element from Taihu (TH) is Al, which is significantly higher than that in other water areas. Multivariate analysis selected different spatial distribution patterns in four discriminative element ratios (Pb/Ca, Cr/Ca, Na/Ca, and Al/Ca) in the muscle of <i>H. nobilis</i> in the Yangtze River basin and its related lakes. This study suggests that the screened discriminative elements can be used to visually distinguish different sources of <i>H. nobilis</i> and to quickly trace and verify the origin of newly emerging samples. Therefore, the use of selected discriminative element fingerprint features to trace the origin of new samples has been proven to be feasible. By further discriminating and verifying the muscle element fingerprints of new samples, the discrimination rate is high. Therefore, a multivariate analysis of muscle element fingerprints can be used for tracing the origins of samples of unknown origin in market supervision.