Human bones are easily degraded due to the acidic soil and temperate climate in regions like Japan. Therefore, it is challenging to obtain genetic information about humans from a wide range of ages and regions. In recent years, it has been shown that human and Neanderthal DNA can be recovered from the sediment of archaeological sites. However, there is a lack of fundamental research on the origins and behaviour of that DNA. In this study, DNA was extracted from the human bones of two individuals and their surrounding sediments at Katsuren Castle in Okinawa, Japan, dating from the mid-11th to early 13th centuries CE. We analysed human mitochondrial DNA sequences from the sediments and compared them with those of the bones. As a result, the human mitochondrial haplogroups obtained from the sediments were almost identical to the mitochondrial haplogroups obtained from the human bones. Furthermore, the degradation pattern, which is a characteristic of ancient DNA, was also observed. These results suggest that even at burial sites where no human remains have remained, it may be possible to extract past human genetic information by extracting DNA from the sediments in the burials.