The initial step in prokaryote species and genera descriptions is now largely based on the 16S rRNA gene sequencing approach followed often by a very restricted additional phenotypic characterisation of the representatives of the potential novel taxa. Despite the advantages of the sequence-based approaches, there appears to be a tendency to classify new species on the basis of comparative sequence analyses of 16S rRNA gene sequences and other gene sequence data (multilocus sequence analyses, MLSA), contrary to the indications of other data. However, the biological meaning behind these sequence data is not always clear, and one should be careful with comprehensive taxonomic rearrangements until there is better insight of these data.