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In this study, we typed 51 male individuals from North Borneo using 17 Y-chromosome STRs contained in the AmpFLSTR® Yfiler ® kit (Applied Biosystems). These indi¬viduals constitute five indigenous ethnic populations repre¬senting the three major linguistic groups (Dusunic, Murutic and Paitanic): the Dusun (n-7), Rungus (n-12), Sonsogon {n-12), Murut Paluan {n-12), and Sungai Lingkabau Paitan (n-8). A total of 37 haplotypes were identified, of which 30 individuals were represented by a single haplotype. The mean ± S.D. haplotype diversity was 0.600+0.181 and the discrimination capacity was 0.725. The results also showed that the haplotype H33 was the most frequent hap¬lotype observed in the sampled male populations occurring exclusively in the Murut population. Comparative analysis between Y-haplotype populations of North Borneo and the ethnic populations (Bidayuh, Iban, and Melanau) of neigh¬bouring Sarawak (East Malaysia) i.e. indicated that the Sungai Lingkabau Paitan was more closely associated with the Melanau with respect to Y-haplotype descent (RST=- 0.0023). In addition, the Multidimensional Scaling (MSD) analysis managed to clearly differentiate the eight groups from Borneo. We concluded that the 17 Y-chromosome STRs data of North Bornean populations are valuable resources in the ap¬plications of forensic and population genetics of the ethnic groups.