We describe a rapid and robust assay to genotype mitochondrial deoxyribonucleic acid (mtDNA) coding region single nucleotide polymorphism (SNPs) using the SNaPshot (Applied Biosystems, Foster City, CA) minisequencing reaction kit. A protocol for mtDNA SNaPshot typing is described in detail, although we emphasize that this method allows great flexibility in the implementation of whatever set of mtDNA SNPs. We discuss the utility of our selection of mtDNA SNPs for molecular anthropologists and forensic geneticists. Firstly, these SNPs allow allocating common mitochondrial West Eurasian haplotypes into their corresponding branches of the mtDNA skeleton, with special attention to the subdivision of sequences belonging to haplogroup H, the most frequent European haplogroup (40-50%) and the worst phylogenetically characterized in the first and second hypervariable segments (HVS-I/II; by far, the most common segments analyzed by sequencing). Second, the polymorphic positions selected for this multiplex reaction considerably increase the discrimination power of current mitochondrial analysis in the forensic field. The method shows high accuracy and robustness, avoiding both the use of alternative time-consuming classical strategies (i.e., restriction fragment length polymorphism typing) and the requirement of high quantities of DNA template.