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In addition, the analysis of genetic variations also provides detail knowledge for understanding the ancient human demographic history. The admixtures within individual may affect the interactions between complex genes with other genes and environmental factors, and at the same time, also affect the susceptibility of individual to particular diseases (Collin et al. Recent studies have highlighted the importance of characterizing the genetic make-up of admixed populations (Sankararaman et al. The knowledge of population genetic structure and genetic ancestry hold great potential towards better understanding of the differential susceptibility to disease, response to drugs and complex interaction of genetic and environment factors (Collin et al. These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided valuable information on the enigmatic demographical history as well as shed some insights into the origins of the Malays in the Malay Peninsula. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced back to have shared a common ancestor with the Proto-Malays and Chinese. More than 98% of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly admixture pattern among populations. We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. We also have included in the analysis 12 other study populations from Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian SNP Initiative (PASNPI) Consortium and International HapMap project database. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu Minang, Melayu Kedah, and Melayu Kelantan. The sub-ethnic groups can be divided based on the region they inhabit the northern ( Melayu Kedah and Melayu Kelantan), western ( Melayu Minang) and southern parts ( Melayu Bugis and Melayu Jawa) of Peninsular Malaysia. The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago.