When species are endangered, rare, or hard-to-sample, noninvasive sampling methods may prove useful for the purposes of genetic studies or for collecting evidence of the presence of a species. We developed and applied a molecular protocol to rapidly distinguish two syntopic species of Galápagos land iguana (Conolophus marthae and C. subcristatus) using stool samples. We used PCR for the amplification a short region of the mtDNA control region, followed by a selective restriction reaction. The protocol, relatively inexpensive and easy to use, does not require DNA sequencing. It proved highly efficient when applied on fresh feces, while its efficiency decreased to 17% for those that had been exposed to the environment for several days or weeks. Our protocol will prove useful when feces are used to collect indirect information about the diet and geographic occurrence of C. marthae.