The paper summarises many years of discussions and experience of biodiversity publishers, organisations, research projects and individual researchers, and proposes recommendations for implementation of persistent identifiers for article metadata, structural elements (sections, subsections, figures, tables, references, supplementary materials and others) and data specific to biodiversity (taxonomic treatments, treatment citations, taxon names, material citations, gene sequences, specimens, scientific collections) in taxonomy and biodiversity publishing. The paper proposes best practices on how identifiers should be used in the different cases and on how they can be minted, cited, and expressed in the backend article XML to facilitate conversion to and further re-use of the article content as FAIR data. The paper also discusses several specific routes for post-publication re-use of semantically enhanced content through large biodiversity data aggregators such as the Global Biodiversity Information Facility (GBIF), the International Nucleotide Sequence Database Collaboration (INSDC) and others, and proposes specifications of both identifiers and XML tags to be used for that purpose. A summary table provides an account and overview of the recommendations. The guidelines are supported with examples from the existing publishing practices.