The access to molecular collections worldwide greatly improves the quality of scientific research by making a growing number of data available for investigation. The efforts on digitisation also aim at facilitating the exchange of material between institutions and researchers that must follow regulations in place and respect best practice. The handbook presented here proposes a workflow to follow to safely exchange materials, in accordance with international laws and legislation. We make numerous recommendations here to help the institutions and researchers to navigate the legal and administrative procedures, in order to manage molecular collections in the best way possible.