This dataset contains data of the occurrence of macrozoobenthos which was recorded at survey sites of the Monitoring Sites 1000 Projects: Coastal Area Survey (Tidal flats). The annual survey was carried out with eight places of Japanese coast from north (Hokkaido) to south (Okinawa). In addition, the data about reference specimens in the survey every five years is included. The data of this dataset is derived from the data file of the Monitoring Sites 1000 Projects: Coastal Area Survey. The data file includes the information about quantity data of macrozoobenthos (the number of individuals per quadrats).