Due to the difficulties in deep sequencing, high-throughput sequencing of ancient DNA has been limited to exceptionally well-preserved ancient materials. The primary factor is microbial attack popularly observed in the buried materials, and it causes drastic increase in relative ratio of microbial DNA in the extracted DNA. We present a unified strategy in which emulsion PCR is coupled with target enrichment followed by next-generation sequencing. The method made it possible to obtain efficiently non-duplicated reads mapped to target sequences of interest, and this can achieve deep and reliable sequencing of ancient DNA from typical materials, even though poorly preserved.