To examine diurnal variations in fluorescent dissolved organic matter in the surface seawater, we carried out incubation experiments using surface seawater collected from the subtropical Pacific, coastal area in Shimoda, Shizuoka, Japan, and bay area in Misaki, Kanagawa, Japan. The amplicon sequence data were obtained from bacteria assemblages in the seawater samples used for the experiments to examine the composition of bacteria groups in each experiment.