Human leukocyte antigens (HLA) are important genetic markers of tissue identity and accurately reflect ancestral history. The work reported in this paper provides a detailed description of HLA polymorphism in Polynesian and Maori individuals in relation to other populations. Our study concerns HLA classes I and II antigens in Polynesian (N =36) and Maori (N =114) subjects genotyped at two digit resolution by New Zealand Blood Service Laboratory in Auckland using polymerase chain reaction-sequence specific oligonucleotide and PCR-SSP technologies. We have also compared our data with those from other Austronesian-speaking Mongoloid and Papuan-speaking Australoid populations in order to test previously published account of the origin of Proto-Polynesians via gender-biassed gene flow between these two ancestral populations. We use principal coordinate analysis for this purpose, arguing this approach to be superior to tree-based methods, because of factors associated with population history and admixture. Our data are in general agreement with earlier work and reflect received wisdom on the dual origin of Proto-Polynesians. They also show the way in which the genetic make-up of Polynesian and Maori subjects is changing due to intermarriage with Europeans.