Squirrel monkeys, mainly Saimiri sciureus and S. boliviensis, are common in zoos and widely used in biomedical research. However, an exact species identification based on morphological characteristics is difficult. Hence, several molecular methods were proposed, but all of them are expensive and require extensive laboratory work. In contrast, we describe an Alu integration, which is present in S. boliviensis boliviensis and absent in S. sciureus. Among analyzed S. b. peruviensis specimens various presence/absence patterns of the integration were detected indicating that this study population might have originated from a natural hybrid zone. Based on the size of the Alu element (∼300 bp), the presence/absence pattern of the integration can easily be traced by PCR and followed by agarose gel electrophoresis. Am. J. Primatol. 70:1177–1180, 2008. © 2008 Wiley-Liss, Inc.