Comparative 16S rRNA sequence analysis has demonstrated that the genus Bacillus consists of at least five phyletic lines. rRNA group 3 bacilli of Ash, Farrow, Wallbanks and Collins (1991) comprising Bacillus polymyxa and close relatives is phylogenetically so removed from Bacillus subtilis, the type species of the genus and other aerobic, endospore-forming bacilli that they warrant reclassification in a new genus Paenibacillus. The genus Paenibacillus can be readily distinguished from other Bacillus groups using a battery of phenotypic characters and a highly specific gene probe based on 16S rRNA.

The taxonomic status of the type species of the genus Paenibacillus cannot be easily determined according to the rules of the Bacteriological Code since the rules may be interpreted in an ambiguous way. Depending upon how the rules are applied the type species may be either Paenibacillus polymyxa or Paenibacillus durus. In addition, depending upon the way in which the Bacteriological Code is interpreted, the question of whether the name P. durus (Collins et al. 1994) has been validly published must also be addressed.