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.