Relatively few data exist on population differences in the vocal behavior of mammals. Geographic variation in calls is of special interest because of the implications for resolving evolutionary and behavioral questions. For example, information on geographic variation in vocalizations complements morphological and molecular data used to infer phylogenetic relationships and provides evidence for the mechanisms underlying call development. A quantitative acoustic analysis of orangutan long calls was undertaken, comparing flanged adult males from four geographically distinct sites across Borneo and Sumatra, revealing consistent differences among the calls of individuals. Long calls produced by orangutans from the four sites in Borneo and Sumatra differ in quantitative acoustic measures. Discriminant function analysis reveals that acoustic variables can be used in combination to assign calls to the correct individual, site and island at rates higher than that expected by chance. Specifically, four acoustic parameters proved reliable for distinguishing among the individuals, between sites, and across the two islands that arguably represent populations from separate species or subspecies. Although Bornean and Sumatran long calls share a repetitive structure and show similar call rates (0.100–0.500 LCs/h) and maximum frequency bands (0.400–1.500 kHz), they differ significantly in the number of pulses per call, call speed, call duration, bandwidth, pulse duration, and dominant frequency. Strong consistency in these acoustic parameters is also seen among males within sites and the observed variation may allow for individual recognition. Individual identification by call structure presumably benefits dispersed orangutans, where individuals characteristically forage independently and both encounters and interactions with signaling males are highly variable and largely dependent on context. Acoustic recognition of callers facilitates the choice of which males to join or avoid, thus allowing receivers to manipulate potential costs and benefits of association.