Parasitic remains in paleofeces can be an indicator to infer the health and sanitary conditions of ancient people. Species identification using microscopic observation depends on the condition of the remaining eggs. In addition, identification by polymerase chain reaction (PCR), a molecular biological method, is challenging because ancient DNA extracted from paleofeces is very short and fragmented, and the amount of remaining DNA is often extremely poor. Massively parallel sequencing using next-generation sequencer (NGS) has become common in recent years. Research focusing on ancient infectious diseases based on genomic analysis has also become more active, especially in Europe and its neighboring regions, where typical infectious diseases such as plague, tuberculosis, and leprosy have been reported. With its warm and humid climate, Asia seems to be strongly affected by parasitic infections. However, few genomic analyses have identified diseases in Asian populations. This study was designed to search for ancient parasites in the paleofecal DNAs of the Japanese archipelago and to clarify the ancient environment and their impact on the health of ancient people. We performed ancient DNA sequence analysis using NGS on the paleofeces of the hunter-gatherer Jomon period populations in the Japanese archipelago. A comprehensive search was conducted for various infectious diseases that may have existed in the Japanese archipelago during the Jomon period, with a focus on parasites. This study is aimed at elucidating the living environment and the actual conditions for the transmission of infectious diseases in this region.