The purpose of this project was to determine the species diversity and ecological distribution of the genus Gambierdiscus at two coastal sites in Japan: Kochi Prefecture (temperate area) and Okinawa Prefecture (subtropical area). The data released in this project were used in the paper "Horizontal and vertical distribution of Gambierdiscus spp. (Dinophyceae) including novel phylotypes in Japan identified by 18S rDNA metabarcoding". This data was created from contig sequences derived from raw data from the MiSeq sequencer, as well as primer sequence removal, short sequence removal, unique sequence creation, and count table creation by Mothur. The primers used in this paper were the newly designed Alveolata Primer, which is designed to specifically amplify the 18S rDNA V8-V9 region of the Alveolata superphylum.