Over the past 20 years several studies have attempted to clarify orangutan systematics based on DNA sequences and karyological and morphological data; however, the systematic and phylogenetic relationships among orangutan taxa remain controversial. Surprisingly, few systematic studies have used data from wild-living orangutans of exactly known provenance. Furthermore, most of these studies pooled data from huge geographic areas in their analyses, thus ignoring possibly distinct subpopulations. This study represents a new approach to orangutan systematics that uses orangutan long calls. Long calls are species-specific vocalizations used by many nonhuman primates, and data on their acoustical and temporal structures have been used to assess the relationships among, and phylogenies of, several primate taxa. Altogether, 78 long calls from wild-living orangutans from five populations in Borneo and five in Sumatra were included in the analyses. Aside from the chiefly paraphyletic topology of cladistic results, which neither support nor reject a Borneo-Sumatra dichotomy, bootstrap values support three monophyletic clades (northwest Borneo, northeast-east Borneo, and Ketambe) that corroborate geographic groups. The shortest trees and multivariate analyses provide some support for a closer relationship between Sumatran and specific Bornean demes than between particular Bornean demes themselves, indicating that conservation management should be based on orangutans from different populations rather than on just the two island-specific groups.