We combined the metabarcoding data of various coastal ecosystems and a newly developed trait-based approach to study the link between taxonomic and functional diversity across marine protistan communities of different size-classes. Environmental DNA was extracted and the V4 18S-rDNA genomic region was amplified and sequenced. In parallel, we developed a new theoretical framework of 30 biological traits, which cover the diversity and variety of marine protistan ecological strategies. Operational Taxonomic Units (OTUs) and their taxonomic reference (represented in the present table) from our metabarcoding dataset were associated with the 30 biological traits, using published and accessible information on protists (also referenced in the table). Three version of the table are available, 1) the full annotation table with references of annotations at the right of the table, 2) the full annotation table adapted to software R and 3) a reduced version with only 13 traits (also adapted to R), that was used in the cited publications.