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Keywords:

  • algae;
  • biological names;
  • codes;
  • integrative taxonomy;
  • protozoa;
  • protistan

Nomenclature of microbial eukaryotes has been historically relegated to secondary importance. This is a legacy of the traditional classification of life into the most studied multicellular forms (plants, fungi, and animals). Despite the revolution in an understanding of eukaryotic diversity and relationships that has been achieved as a result of the use of molecular techniques, the description of microbial eukaryote genera and species is more difficult today than in the past. Researchers are at liberty to choose between the botanical (in the traditional sense) and zoological codes of nomenclature, although there is no obligation to comply with either. We demonstrate that, by combining the foci of different nomenclature codes with the current knowledge of relationships, a large number of genera and species end up being regulated by two codes (Patterson's ambiregnal taxa) and, in some cases, may even be regulated by none. We briefly present historically proposed types of solutions to this problem, and propose that an elaboration of authoritative guidelines to regulate the nomenclature of microbial eukaryotes by the community of researchers is most appropriate at this time. Most importantly, we plead to the community of researchers to resolve this centuries old outstanding issue. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.