Our study presents a new method to unbiasely characterize the mammalian host blood meals of Anopheles mosquitoes by targeted high-throughput sequencing of the mammalian mitochondrial 16S rRNA gene. In addtion, we also evaluate the number of human individuals fed on by amplifying a 300bp fragment of the human mitochondrial hypervariable region I. Overall, our approach provides a comprehensive strategy to evaluate the mammalian host source of mosquito blood meals and could be applied to study the blood meals of other athropod vectors as well.