The scientific species reference is based on the World Reference Marine Species (WoRMS) and on Fishbase for fish. WoRMS is the taxonomic reference system recognised by the international scientific community and recommended for ICES reporting.

As in WoRMS, the Harmonie repository is hierarchical and follows the taxonomic tree (species, genus, family, order, etc.). In addition to the scientific name and the systematic level of the species, the authority and the AphiaID (unique identifier of WoRMS) are stored in Harmonie. Given the rapid evolution of taxonomy, the notion of referent or synonymous taxa is managed.

For individuals measured in the various collection actions, the scientific species are linked to the size-weight relationship reference system. These allow the consistency between height and weight measurements for an individual or a sample to be checked during data entry, or to estimate one of the two parameters if it could not be observed.

Additions and modifications are made as and when requested by users. Updates are validated by experts in the field before being implemented in the database.