Taiwan has been considered as the homeland for the expansion of Austronesian (AN)-speaking populations that spread from Easter Island to Madagascar. However, recent evidence from human genetic data have reached conflicting conclusions. Here, I studied the genetic affinities among current inhabitants of Taiwan and their closely related ethnic groups. Our lab genotyped 94 individuals residing in Taitung county of Taiwan using Illumina's Omni2.5Exome array (~2.5 million SNPs). In order to maximize the number of Asian populations in our analyses, I merged our data with three public SNP datasets - the Human Genome Diversity Project (HGDP), Pan-Asian SNP Consortium, and Southeast Asia dataset. Overall, the merged dataset includes 2,610 individuals across 124 ethnic groups. I performed principle component analysis (PCA) to identify patterns of genetic variation across all samples. As a result, the individual distribution on the first two PCs display a gradient of population substructures along the longitudes of population sampling locations across continents. In addition, I found signatures of admixture between Taiwanese Han and aborigines. I further inferred a maximum-likelihood tree that best fits the observed covariance matrices of allele-frequency distributions between all the populations analyzed. AN-speaking populations in the Island Southeast Asia (ISEA) and Taiwan formed a monophyletic clade. Moreover, the branch of Taiwanese aborigines appears to derive from the ISEA populations, suggesting that AN ancestors might be originated from ISEA, and then migrated to Taiwan. The result is inconsistent with the “Out of Taiwan” hypothesis.