The primary work in FishBOL is led by ten Working Groups that take responsibility for overseeing collections, identifications and barcoding of the fish faunas in their region.

These regional Working Groups (WGs) included:

Each WG covers both fresh water and marine partitions.

The WGs consist of a team of researchers, with a nominated leader. They reviewed the list of species generated for their area using FAO data (with FishBase assistance), and keep records of their barcoding involvement (collections, vouchers, sequencing), in order to minimize duplication.

The global FISH-BOL campaign is overseen by: