High-frequency eDNA metabarcoding survey data of coastal fish across the Japanese Archipelago

The Japanese archipelago, spanning over 3,000 km from subarctic to subtropical zones (approximately 24°N to 45°N), hosts a diverse array of coastal fish communities shaped by pronounced latitudinal gradients. Here, we present a high-frequency environmental DNA (eDNA) metabarcoding dataset of coastal fishes collected across the archipelago. Using the MiFish primer set targeting a hypervariable region of the mitochondrial 12S rRNA gene, we conducted surveys at 195 sites, yielding 690 samples collected through one-time (annual), monthly, and biweekly sampling schemes. The inclusion of high-frequency sampling enabled the detection of fine-scale temporal variations in fish community composition. From January 2018 to March 2019, eDNA samples were collected along with metadata on geographic and environmental variables, including coastal structure, wave height, tide, currents, and water temperature. The resulting dataset comprises fish eDNA records for 1,477 species across 171 families. This dataset offers a valuable resource for investigating fish community structure, temporal dynamics, and biodiversity in the coastal ecosystems of the Japanese archipelago, supporting a range of applications in ecology, conservation, and eDNA-based research.