Vocal characteristics have been used extensively to distinguish different taxonomic units of gibbons (family Hylobatidae). The agile gibbon (Hylobates agilis) has a disjunct distribution range in the Southeast Asian archipelago (remnants of the former Sunda landmass), and populations on different islands are currently recognized as distinct subspecies or even species. We recorded great calls from female agile gibbons from two populations on Sumatra and two populations on Borneo and examined the vocal variability on four levels: within-individuals, between-individuals, between-populations and between-islands. The primary objective was to evaluate the effect of geographical isolation on variability in song pattern and to test whether proposed island-specific song characteristics exist, reflecting evolutionary divergence between Sumatran and Bornean agile gibbons. One hundred great calls were recorded from 20 females and analyzed for 18 spectral and temporal acoustic parameters. Principal component analysis followed by a nested ANOVA on components revealed a complex pattern of song variability not likely to reflect taxonomic or evolutionary relationship. We found no evidence that Sumatran and Bornean agile gibbons have evolved different vocal characteristics, refuting a distinction between them based on vocal characteristics. A high level of plasticity was found in great calls from the same individual, and generally the inferred pattern of variability suggested that ecological or social factors may confound any genetically based island dialects.