This guide provides a framework for generating and disseminating voucher-based DNA reference barcode sequences. It provides a general step-by-step approach to collecting and processing specimens/vouchers, as well as generating and reporting the resulting nucleotide sequence data. We describe protocols for molecular lab work for generating both reference gene sequences (“barcodes”) as well as genome skimming to derive full mitogenomes and nuclear ribosomal repeat regions (“ultra-barcodes”). Our guiding principles include FAIR (Findable, Accessible, Interoperable, Reusable) and CARE (Collective Benefit, Authority to Control, Responsibility, and Ethics) data practices to ensure resulting specimen and sequence data will be publicly accessible. We intend these guidelines to be useful for both novice and expert systematists and molecular biologists alike. Here we focus our examples on marine taxa and habitats, but this resource is widely applicable to most aquatic and terrestrial biodiversity and environments. We invite interested readers to study the Resources Section for a more in-depth treatment of the subject matter. This work is led by the West Coast Ocean Biomolecular Observing Network (WC-OBON), a project under the Ocean Biomolecular Observing Network Programme (OBON), sponsored by the United Nations Decade of Ocean Science for Sustainable Development 2021-2030 (U.N. Oceans Decade).