In this study, we investigated marine sediment from around the Okinawan 'Kaichu-Doro' Causeway, which was constructed 44 years ago to connect three islands (Henza-jima, Miyagi-jima, Hamahiga-jima) to Okinawa. The construction of this causeway has been shown to influence the surrounding marine ecosystem via fragmentation and the loss of water circulation. In this research, we collected 10 sediment cores (5 cores from each side) 60-80 cm length from 1 m water depth and divided into layers (each layer 15 cm) to examine differences in environmental DNA from areas around the causeway. We examined the vertical diversity of microbial communities and metabolite to elucidate and estimate the correlation between metabolites and microbial communities among marine sediment layers.