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The red panda (Ailurus), a rare and endangered mammal native to the Himalayan–Hengduan Mountains, has a specialized bamboo diet. Combining morphological and genomic evidence, red pandas have been classified as Ailurus fulgens and Ailurus styani. However, previous studies focused on ecological aspects such as foraging behaviors, habitat use and threats within specific distributions; hence, there is still a gap in quantitative comparative studies on the trophic niches of these two species. In this study, we calculated and compared the isotopic trophic niche widths of A. styani and A. fulgens by measuring carbon and nitrogen stable isotopes in hair keratin of 102 red pandas, then conducting a fecal analysis to explore the diet of a population. The results showed that (1) there was no significant difference in δ13C values between A. styani (−24.73 ± 1.26‰, N = 86) and A. fulgens (−24.43 ± 1.20‰, N = 16); however, A. styani had 1.4‰ higher average δ1⁵N value than that of A. fulgens, and the isotopic niche widths converted by Bayesian ellipse model were A. styani SEAC = 4.40‰2, A. fulgens SEAC = 4.70‰2, which might be caused by their lower and narrower altitude distribution. (2) Niche widths of three genetic populations in A. styani were XXL-LS (5.16‰2), EH-GLG (3.40‰2), QL (2.31‰2), and the comparison of the fecal composition suggested their diet diversity, which might imply a degree of competitive pressure with sympatric animals. (3) Sichuan red pandas occupied a lower trophic position compared to other herbivores but higher than giant pandas in the same ecosystem, and the niche width of red pandas was two times larger than that of sympatric giant pandas, which was related to the foraging strategies and microhabitat selection of the giant and red panda. This research provides basic stable isotopic data for red pandas, offers scientific support for the differentiated and refined conservation and management of the red panda and its habitat, and develops the application of stable isotope analysis in the ecological studies of endangered species.