The present paper reports the development of a public project addressed to build up and publish a DNA barcode reference library for the animal species occurring in Italy listed in the II, IV and V Annexes of the “Habitats Directive” 92/43/EEC. DNA barcoding is a global standard, namely a procedure based on a gene sequence located in a standardized genome region as a diagnostic biomarker for species. DNA barcodes data have been either produced in our laboratories or collected from the literature and international gene databases. They were subsequently used to assemble a database containing both genetic data and information related to the origin of the data. This project represents the first pilot store of DNA sequence data built-in interoperability within the portal of the National Network of Biodiversity of the Italian Ministry of the Environment. The archive, called "DNA Barcode Database of Italian Nature 2000 animal species" (owned by the Zoology and Evolutionary Biology group at Tor Vergata University), was implemented in a relational DBMS with a free license program (PostgreSQL v9.3.4), mapped using the schema ABCD and the extension DNA, and then made interoperable using the software BioCASE (v3.6.0).