In order to clarify the process of biogeographical evolution of the Bornean white-bearded gibbon (Hylobates albibarbis), I examined genetic constitution of this gibbon and its genetic relationship to H. agilis of Sumatra and H. muelleri of Borneo by analysis of amplified fragment length polymorphism (AFLP). DNA samples from albibarbis (n=18), agilis (n=14) and muelleri (n=14) were examined. Two samples of H. lar and 6 samples suspected of interspecies hybrids were also analyzed for comparison of AFLP profiles. All the gibbons studied here had been identified by morphological features, chromosomal variations and mtDNA. Three primer combinations (EcoRI-AGG/ MseI-CTC, EcoRI-ACG/ MseI-CAC, and EcoRI-ACA/ MseI-CTA) were used in the selective amplification. A total of 216 fragment sites were scored and used in population genetic analysis. Pairwise Φ_PT showed significant differentiation among albibarbis, agilis and muelleri, suggesting that they are distinct taxonomic units. Nei’s genetic distance was estimated to be 0.040 between albibarbis and muelleri and 0.049 between albibarbis and agilis. The result of principal coordinate analysis indicated that each taxonomic unit formed a distinct cluster, and that the albibarbis cluster intervened between the clusters of agilis and muelleri, suggesting that genetic constitution of albibarbis would be intermediate state between agilis and muelleri.