In 2015, we released a comprehensive annotation update for RefSeq prokaryotic genomes in order to harmonize genome annotation and complete the transition to the new protein data model. A new prokaryotic protein name database, name specifications, and an evidence-based strategy were developed and are currently in the process of being deployed. Thus far, over 3 million protein records have updated names in an initial demonstration of the approach. The new prokaryotic data model offers a significant advantage to name management as the protein name is carried with the protein sequence record; updating the name on that protein record results in automatically propagating the update to all genomes that are annotated with that accession number.