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The illegal wildlife trade is a significant threat to global biodiversity, often targeting already threatened species. In combating the trade, it is critical to know the provenance of the traded animal or part to facilitate targeted conservation actions, such as education and enforcement. Here, we present and compare two methods, portable X-ray fluorescence (pXRF) and stable isotope analysis (SIA), to determine both the geographic and source provenance (captive or wild) of traded animals and their parts. Using three critically endangered, frequently illegally traded Philippine species, the Palawan forest turtle (<i>Siebenrockiella leytensis</i>), the Philippine cockatoo (<i>Cacatua haematuropygia</i>), and the Philippine pangolin (<i>Manis culionensisis</i>), we demonstrate that using these methods, we can more accurately assign provenance using pXRF data (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mover accent="true"><mi>x</mi><mo>¯</mo></mover><mo> </mo></mrow></semantics></math></inline-formula> = 83%) than SIA data (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mover accent="true"><mi>x</mi><mo>¯</mo></mover><mo> </mo></mrow></semantics></math></inline-formula> = 47%). Our results indicate that these methods provide a valuable forensic tool that can be used in combating the illegal wildlife trade.