We analyzed a marine sediment core from Beppu Bay, Oita Prefecture using environmental DNA metabarcoding with universal primers targeting fish and mammal. The DNA fragments dating back approximately 1,900 years were detected, showing that eDNA can persist in seafloor sediments over long timescales and can help reconstruct past biotic communities. We sectioned the sediment core at 1 cm intervals, and extracted DNA from each layer. Because sediment age varies with depth, each subsample represents a different time period. We found that genus richness peaked between AD 500 and 1000 and then declined markedly toward the present, while total read numbers were much higher in the modern layers, indicating that DNA preserved more in modern sediments. We also found that primer-specific patterns differed. MiFish detected a total of 39 genera, but high read numbers were observed across sediment ages. Cyprinidae and Salmonidae were frequently detected in the modern layers, suggesting the possible effects of aquacultural production around Beppu Bay. The Japanese water shrew was repeatedly detected from around AD 200 through modern strata, and wild boar was also detected in the older layers, implying that river-derived DNA may also have been transported and accumulated in marine sediments. Mimammal detected 192 genera, but high read numbers were mainly confined to recent layers. In addition to fish detected by MiFish, diverse marine taxa, such as macroalgae, plankton, and ascidians, were also detected, highlighting the differences in PCR amplification and detection characteristics among the primer sets. Biodiversity declines have been generally linked to environmental pollution, since the rapid economic growth period beginning in the 1950s, and to recent rapid climate change. Our results, showing reduced biodiversity toward the present, are consistent with these reported trends.