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The Yama area is characterized by numerous large-scale fluorite–quartz veins that are located along faults within the widespread Late Devonian–Late Silurian syenogranites in the Tataleng granitic batholith, Qilian Orogen, Northwest China. These fluorite–quartz veins contribute to an important fluorite reserve, but their ore genesis remains unresolved so far. In this study, trace elements, rare earth elements (REEs), and hydrogen, oxygen, and strontium isotopic compositions of fluorites are analyzed. The studied fluorite samples have similar chondrite-normalized REEs, including Y patterns, with relatively strong enrichment in heavy REEs, negative Eu anomalies, strongly positive Y anomalies, and comparably invariable Y/Ho ratios of 41.43–73.79, suggesting a unique hydrothermal genesis. The relatively variable values of δD and δ¹⁸O are −77.4‰ to −102.4‰ and −12.7‰ to −4.3‰, respectively, close to the meteoric water line. These fluorites yield relatively invariable analytical ⁸⁷Sr/⁸⁶Sr ratios of 0.749089−0.756628 (except for an anomalously high ratio), and their calculated initial ⁸⁷Sr/⁸⁶Sr ratios, based on the ore-forming ages provided, are apparently higher than the calculated initial ⁸⁷Sr/⁸⁶Sr ratios of syenogranite wall rocks. Collectively, the geochemistry of trace elements, REEs, and stable isotopes (H, O, and Sr) suggests that the ore-forming fluids were of meteoric origin and that the Sr sources were directly derived from the ore-forming fluids themselves rather than syenogranite wall rocks. Finally, it was considered that the Yama fluorite deposit is a fault-controlled hydrothermal vein-type deposit which was possibly related to the evolution of the Paleo-Tethys Ocean in the Permian–Triassic.