With the aim of better understanding human origins, history and relationships, we use molecular biology techniques to study the genetics, history and migration of human populations across the world. Of particular focus is the Philippines in Southeast Asia which is situated along proposed historical and pre-historical migration paths of various human populations in the Asia-Pacific region. The Philippine archipelago is composed of over 7,000 islands with the human population being divided into 17 geo-politically defined regions and over 100 ethno-linguistic groups. This diversity in terms of geography, people, culture and language has never been extensively studied in the context of human genetic origins, relations and population migration. This same diversity may have been the result of the archipelago being either a simple passage way or even a site for further development of various human populations that have spread into this region of the world. Through the analysis of autosomal, Y-chromosome and mitochondrial DNA markers, we study various Philippine population groups to gain insight into the country’s human genetic diversity, and to correlate this with the peopling of the archipelago and with how this particular region of the world was populated.