We have developed a single PCR multiplex SNaPshot reaction that consists of 32 coding region SNPs that allows (i) increasing the discrimination power of the mitochondrial DNA (mtDNA) typing in forensic casework, and (ii) haplogroup assignments of mtDNA profiles in both human population studies (e.g. anthropological) and medical research. The selected SNPs target the East Asian phylogeny, including its Native American derived branches. We have validated this multiplex assay by genotyping a sample of East Asians (Taiwanese) and Native Americans (Argentineans). In addition to the coding SNP typing, we have sequenced the complete control region for the same samples. The genotyping results (control region plus SNaPshot profiles) are in good agreement with previous human population genetic studies (based on e.g. complete sequencing) and the known mtDNA phylogeny. We observe that the SNaPshot method is reliable, rapid, and cost effective in comparison with other techniques of multiplex SNP genotyping. We discuss the advantages of our SNP genotyping selection with respect to previous attempts, and we highlight the importance of using the known mtDNA phylogeny as a framework for SNP profile interpretation and as a tool to minimize genotyping errors.